eRibo Pro Summary Report

This interactive report provides an overview of eRibo Pro results, accessible at the different tabs. For each table and plot, the button can be clicked to get more information. The menus in the top right corner of each plot can be used to modify the plots (zoom, hide samples, and save a copy of the plot). This report is optimized for viewing on a desktop and plots have been tested on several browsers but in some cases they may not render correctly, please use an alternate browser if plots do not load.

If you are interested in performing your own eRibo Pro experiment please contact us.

Experiment Summary

This report summarizes an eRibo Pro experiment where HEK293 cells were treated with either Torin, a translation inhibitor, or a DMSO control. Full methods details are available upon request. The following samples are included in the analysis:

Sample group	RPF	RNA-Seq
Treated	RPF_Torin_Rep1, RPF_Torin_Rep2	RNASeq_Torin_Rep1, RNASeq_Torin_Rep2
Untreated	RPF_Untreated_Rep1, RPF_Untreated_Rep2	RNASeq_Untreated_Rep1, RNASeq_Untreated_Rep2

This tab summarizes quality control metrics for the RNA-Seq and ribosome protected footprint (RPF) libraries.

Quality Control Metrics

The following table shows important quality control metrics for each sample. Two libraries are made for each sample, one containing ribosome protected footprints (RPFs) and one from the whole transcriptome (RNA-Seq). For each sample ("Sample"), two rows are included that list the metrics for each library. The identity of the library is included in the "Library" column. The following columns describe the processing of the libraries:

Initial reads: the number of sequenced reads for each library.
% Pass trim: reads first underwent adapter trimming to remove both adapters and sequences shorter than 18 nucleotides. The percentage of sequenced reads that passed this trimming step is listed in this column.
% Repetitive elements: trimmed reads are aligned to Eclipsebio's custom database of repetitive elements. This database includes rRNAs, tRNAs, snoRNAs, and other features. The percentage of trimmed reads that were filtered is listed in the column.
% Uniquely aligned to the genome: the remaining reads from the repetitive element filtering were aligned to the genome, and the percent of those reads that map uniquely to the genome is listed in this column.
% PCR duplicates: PCR duplicates were defined as uniquely mapped reads that map to the same read coordinates and have an identical unique molecular identifier (UMI). The percentage of mapped reads that were identified as PCR duplicates is included in this column.
Final reads: this column lists the number of uniquely mapped, deduplicated reads that were used for this analysis.

Sample	Library	Initial reads	% Pass trim	% Repetitive elements	% Uniquely aligned to the genome	% PCR duplicates	Final reads
RPF_Torin_Rep1	RPF	106,375,285	87.89	42.8	62.79	28.12	24,135,715
RPF_Torin_Rep2	RPF	96,961,854	87.17	44.95	63.18	25.37	21,938,930
RNASeq_Torin_Rep1	RNA-Seq	67,148,202	99.17	14.51	85.78	19.02	39,548,918
RNASeq_Torin_Rep2	RNA-Seq	66,921,389	99.06	14.71	85.81	20.07	38,778,304
RPF_Untreated_Rep1	RPF	100,440,695	88.91	37.24	63.61	27.77	25,748,524
RPF_Untreated_Rep2	RPF	92,265,022	89.5	36.5	62.03	27.44	23,598,327
RNASeq_Untreated_Rep1	RNA-Seq	76,244,094	99.38	15.04	85.77	20.40	43,943,636
RNASeq_Untreated_Rep2	RNA-Seq	62,247,281	99.38	15.22	85.97	19.87	36,129,570

Gene Coverage Range

Pairs of ribosome protected footprint (RPF) and RNA-Seq libraries were prepared from each sample. The plot below shows the distribution of RPM (reads per million) normalized gene counts in each of the libraries.

RPF Periodicity

This plot shows the location of scaled read ends that have been corrected for their estimated P-site (the second binding site for tRNA in the ribosome) from the ribosome protected footprint (RPF) libraries. This correction is to show where ribosomes are directly binding, as the sequenced read ends have an overhang past the ribosome complex. RPF libraries are expected to show a trinucleotide periodicity.

This tab shows the identified differential genes from the RNA-Seq libraries. The comparison for this analysis is Treated (RNASeq_Torin_Rep1, RNASeq_Torin_Rep2) over Untreated (RNASeq_Untreated_Rep1, RNASeq_Untreated_Rep2). All analyses on this tab were performed on a whole gene level.

RNA-Seq Volcano Plot

The plot below shows a comparison between fold change and significance in RNA-Seq libraries from Treated and Untreated samples. The x-axis shows the fold change ("log₂(fold change)") and the x-axis shows significance("-log₁₀(adjusted p-value)"). Red (increased in Treated) and teal (decreased in Treated) dots represent genes that are significantly different between conditions. Gray dots represent genes that are not significant. Hovering your mouse over the volcano plot below will show the gene name, Ensembl gene ID, -log₁₀(adjusted p-value), and log₂(fold change) for each point.

RNA-Seq Differential Expression Table

We used a differential expression analysis tool called DESeq2 to compare Treated and Untreated samples. The table below lists significantly up- and downregulated genes along with associated DESeq2 metrics. Genes were identified as significantly different if they have an adjusted p-value cutoff < 0.1 (after multiple testing adjustment) and a log₂(fold change) > 1 or < -1. Only genes annotated as protein coding or lncRNA are included in the table. Multimapping reads were removed before the analysis, which may reduce estimates for genes with high pseudogenization or duplication events.

The following columns are included in the table:

Ensembl ID: Ensembl's unique identifier and version of a gene
Gene name: common name for the gene.
baseMean: average DESeq2-normalized counts across all samples and all conditions
log₂(fold change): log₂-transformed ratio of expression between the two conditions
log₂(SE): log₂-transformed standard error
P-value: unadjusted measure of significance
Adjusted p-value: false discovery rate (FDR) adjusted significance
Up/downregulated: classification of expression change based on the significance and fold change

A copy of the table can be downloaded by clicking the button of the desired format (CSV, Excel or PDF)

Ensembl ID	Gene name	baseMean	log₂(fold change)	log₂(SE)	P-value	Adjusted p-value	Up/downregulated
ENSG00000135114.14	OASL	7.83	2.8	1.04	6.81E-03	9.60E-02	Upregulated

RNA-Seq Gene Enrichment

The GO term and KEGG pathway enrichment analyses show which functional gene categories and pathways are enriched in up- and downregulated genes from the volcano plot above. GO and KEGG analyses were performed with clusterProfiler's enrichGO and enrichKEGG functions. Within each domain are boxes for each gene ontology or KEGG term, and within each term are the contributing genes. The color of the gene box is the log₂ fold change between the two sample conditions while the size of the gene box is based off the -log₁₀(adjusted p-value) for the comparison. The color and size of the term boxes are based off the sum of all contributing genes. You can click on individual GO categories and subcategories to zoom and view their results in more detail. Clicking on the "Analysis" heading will restore the plot to its original appearance. For each gene box, the hover will show the adjusted p-value for the performed comparison and log₂ fold change of the listed gene. For each term, the hover will show the adjusted p-value for the enrichment analysis and the average fold-change of all genes included in the box. Significance and fold changes are not provided for the domains.

This tab shows the identified differential genes from the ribosome protected footprint (RPF) libraries. The comparison for this analysis is Treated (RPF_Torin_Rep1, RPF_Torin_Rep2) over Untreated (RPF_Untreated_Rep1, RPF_Untreated_Rep2). All analyses on this tab were performed on a whole gene level.

RPF Volcano Plot

The plot below shows a comparison between fold change and significance in RPF libraries from Treated and Untreated samples. The x-axis shows the fold change ("log₂(fold change)") and the x-axis shows significance("-log₁₀(adjusted p-value)"). Red (increased in Treated) and teal (decreased in Treated) dots represent genes that are significantly different between conditions. Gray dots represent genes that are not significant. Hovering your mouse over the volcano plot below will show the gene name, Ensembl gene ID, -log₁₀(adjusted p-value), and log₂(fold change) for each point.

RPF Differential Expression Table

We used a differential expression analysis tool called DESeq2 to compare Treated and Untreated samples. The table below lists significantly up- and downregulated genes along with associated DESeq2 metrics. Genes were identified as significantly different if they have an adjusted p-value cutoff < 0.1 (after multiple testing adjustment) and a log₂(fold change) > 1 or < -1. Only genes annotated as protein coding or lncRNA are included in the table Multimapping reads were removed before the analysis, which may reduce estimates for genes with high pseudogenization or duplication events.

The following columns are included in the table:

Ensembl ID: Ensembl's unique identifier and version of a gene
Gene name: common name for the gene.
baseMean: average DESeq2-normalized counts across all samples and all conditions
log₂(fold change): log₂-transformed ratio of expression between the two conditions
log₂(SE): log₂-transformed standard error
P-value: unadjusted measure of significance
Adjusted p-value: false discovery rate (FDR) adjusted significance
Up/downregulated: classification of expression change based on the significance and fold change

A copy of the table can be downloaded by clicking the button of the desired format (CSV, Excel or PDF)

Ensembl ID	Gene name	baseMean	log₂(fold change)	log₂(SE)	P-value	Adjusted p-value	Up/downregulated
ENSG00000005022.6	SLC25A5	15767.99	-1.49	0.03	0.00E+00	0.00E+00	Downregulated
ENSG00000005206.17	SPPL2B	519.23	-1.09	0.12	4.60E-21	1.24E-19	Downregulated
ENSG00000008988.11	RPS20	693.25	-1.73	0.1	2.07E-62	2.19E-60	Downregulated
ENSG00000009307.17	CSDE1	10876.56	-1.06	0.04	1.32E-181	6.45E-179	Downregulated
ENSG00000011028.14	MRC2	443.39	-1.48	0.13	3.32E-30	1.39E-28	Downregulated
ENSG00000026025.16	VIM	21849.69	-1.82	0.03	0.00E+00	0.00E+00	Downregulated
ENSG00000030582.18	GRN	6762.64	-1.02	0.04	3.80E-120	1.03E-117	Downregulated
ENSG00000049860.14	HEXB	2003.02	-1.06	0.06	3.84E-66	4.24E-64	Downregulated
ENSG00000050555.19	LAMC3	221.58	-1.31	0.17	4.66E-14	7.76E-13	Downregulated
ENSG00000054793.14	ATP9A	504.87	-1.13	0.11	9.79E-23	2.90E-21	Downregulated
ENSG00000060138.13	YBX3	3519.84	-1.16	0.05	3.28E-118	8.58E-116	Downregulated
ENSG00000062524.16	LTK	47.02	-1.11	0.36	2.17E-03	8.53E-03	Downregulated
ENSG00000062582.14	MRPS24	1752.56	-1.04	0.07	1.04E-56	9.41E-55	Downregulated
ENSG00000063177.13	RPL18	8962.39	-1.34	0.08	2.72E-57	2.53E-55	Downregulated
ENSG00000064666.15	CNN2	441.0	-1.19	0.12	9.94E-22	2.79E-20	Downregulated
ENSG00000065150.21	IPO5	9578.8	-1.22	0.04	7.38E-228	5.49E-225	Downregulated
ENSG00000065427.15	KARS1	4534.75	-1.05	0.05	1.03E-114	2.47E-112	Downregulated
ENSG00000065978.19	YBX1	2029.87	-1.43	0.06	1.39E-113	3.23E-111	Downregulated
ENSG00000070756.17	PABPC1	3828.69	-3.04	0.06	0.00E+00	0.00E+00	Downregulated
ENSG00000070915.10	SLC12A3	23.21	-2.08	0.56	2.02E-04	1.01E-03	Downregulated
ENSG00000071082.11	RPL31	1681.15	-1.71	0.07	7.57E-130	2.33E-127	Downregulated
ENSG00000074181.9	NOTCH3	1162.44	-1.62	0.08	4.44E-81	6.60E-79	Downregulated
ENSG00000078053.17	AMPH	309.12	-1.11	0.15	4.82E-14	8.01E-13	Downregulated
ENSG00000079739.17	PGM1	3214.18	-1.21	0.05	2.26E-116	5.82E-114	Downregulated
ENSG00000083845.9	RPS5	5307.49	-1.74	0.05	0.00E+00	0.00E+00	Downregulated
ENSG00000089157.16	RPLP0	1420.84	-1.97	0.08	7.95E-140	2.68E-137	Downregulated
ENSG00000089327.15	FXYD5	605.87	-1.31	0.11	2.71E-33	1.27E-31	Downregulated
ENSG00000089351.15	GRAMD1A	787.12	-1.13	0.1	2.95E-31	1.28E-29	Downregulated
ENSG00000092445.12	TYRO3	306.87	-1.12	0.15	3.89E-14	6.50E-13	Downregulated
ENSG00000095585.18	BLNK	525.67	-1.06	0.12	4.06E-18	9.10E-17	Downregulated
ENSG00000099617.4	EFNA2	32.9	-1.07	0.44	1.41E-02	4.38E-02	Downregulated
ENSG00000100258.18	LMF2	1219.01	-1.16	0.08	1.89E-48	1.38E-46	Downregulated
ENSG00000100979.15	PLTP	1937.65	-1.06	0.07	6.06E-57	5.52E-55	Downregulated
ENSG00000101210.13	EEF1A2	2576.73	-1.09	0.06	3.16E-72	4.03E-70	Downregulated
ENSG00000101444.13	AHCY	6402.39	-1.61	0.04	0.00E+00	0.00E+00	Downregulated
ENSG00000101680.16	LAMA1	1632.35	-1.04	0.07	2.42E-52	1.94E-50	Downregulated
ENSG00000101911.13	PRPS2	2295.79	-1.24	0.06	2.91E-98	5.56E-96	Downregulated
ENSG00000103226.19	NOMO3	118.42	-1.07	0.23	3.19E-06	2.17E-05	Downregulated
ENSG00000103257.9	SLC7A5	4714.69	-1.04	0.05	8.38E-116	2.12E-113	Downregulated
ENSG00000103512.16	NOMO1	478.99	-1.33	0.12	3.47E-29	1.40E-27	Downregulated
ENSG00000103811.18	CTSH	769.89	-1.03	0.09	1.61E-27	6.04E-26	Downregulated
ENSG00000104529.19	EEF1D	2369.02	-1.28	0.06	3.15E-102	6.54E-100	Downregulated
ENSG00000104774.13	MAN2B1	700.73	-1.27	0.1	2.69E-34	1.30E-32	Downregulated
ENSG00000104853.16	CLPTM1	2267.38	-2.08	0.07	9.32E-223	6.59E-220	Downregulated
ENSG00000104863.12	LIN7B	34.48	-1.02	0.42	1.56E-02	4.79E-02	Downregulated
ENSG00000105193.9	RPS16	6212.19	-1.33	0.04	3.31E-203	1.95E-200	Downregulated
ENSG00000105372.8	RPS19	4108.77	-1.5	0.05	2.07E-215	1.39E-212	Downregulated
ENSG00000105409.19	ATP1A3	1712.31	-1.04	0.07	1.04E-56	9.39E-55	Downregulated
ENSG00000105429.13	MEGF8	1270.38	-1.01	0.08	1.20E-39	6.83E-38	Downregulated
ENSG00000105649.10	RAB3A	150.9	-1.12	0.2	4.54E-08	4.00E-07	Downregulated
ENSG00000105726.17	ATP13A1	1833.11	-1.1	0.07	1.25E-61	1.28E-59	Downregulated
ENSG00000106554.13	CHCHD3	2869.09	-1.3	0.05	8.30E-124	2.44E-121	Downregulated
ENSG00000107331.18	ABCA2	505.21	-1.16	0.12	5.01E-22	1.44E-20	Downregulated
ENSG00000108107.15	RPL28	2701.12	-1.75	0.06	7.81E-187	4.09E-184	Downregulated
ENSG00000109475.17	RPL34	1049.96	-1.24	0.08	4.54E-49	3.38E-47	Downregulated
ENSG00000109971.14	HSPA8	12607.21	-1.85	0.04	0.00E+00	0.00E+00	Downregulated
ENSG00000111640.15	GAPDH	18332.79	-2.08	0.03	0.00E+00	0.00E+00	Downregulated
ENSG00000112333.12	NR2E1	30.6	1.02	0.45	2.39E-02	6.86E-02	Upregulated
ENSG00000113504.21	SLC12A7	619.07	-1.09	0.1	2.37E-25	7.83E-24	Downregulated
ENSG00000114391.13	RPL24	3787.34	-1.09	0.05	1.26E-93	2.28E-91	Downregulated
ENSG00000115380.20	EFEMP1	121.32	-1.37	0.23	3.42E-09	3.48E-08	Downregulated
ENSG00000115457.10	IGFBP2	1587.65	-1.01	0.07	2.46E-45	1.68E-43	Downregulated
ENSG00000116251.11	RPL22	295.95	-1.29	0.15	1.14E-17	2.48E-16	Downregulated
ENSG00000116852.15	KIF21B	90.78	-1.06	0.26	5.42E-05	3.05E-04	Downregulated
ENSG00000116962.15	NID1	7915.94	-1.05	0.04	5.62E-146	2.09E-143	Downregulated
ENSG00000118816.11	CCNI	2795.39	-1.31	0.06	1.16E-123	3.35E-121	Downregulated
ENSG00000123143.13	PKN1	1605.97	-1.06	0.07	1.70E-53	1.42E-51	Downregulated
ENSG00000124155.19	PIGT	1648.45	-1.06	0.07	5.57E-57	5.12E-55	Downregulated
ENSG00000125743.11	SNRPD2	6913.68	-1.14	0.04	2.94E-175	1.38E-172	Downregulated
ENSG00000125912.11	NCLN	1844.15	-1.02	0.06	1.95E-58	1.89E-56	Downregulated
ENSG00000127022.16	CANX	19.08	-1.51	0.59	9.86E-03	3.20E-02	Downregulated
ENSG00000129946.11	SHC2	17.83	-2.05	0.63	1.20E-03	5.08E-03	Downregulated
ENSG00000130005.13	GAMT	694.18	-1.22	0.1	7.28E-35	3.60E-33	Downregulated
ENSG00000130203.10	APOE	404.69	-1.15	0.13	1.88E-18	4.30E-17	Downregulated
ENSG00000130226.17	DPP6	14.24	1.47	0.68	3.06E-02	8.45E-02	Upregulated
ENSG00000130313.7	PGLS	973.5	-1.03	0.09	4.72E-33	2.18E-31	Downregulated
ENSG00000130702.15	LAMA5	1122.12	-2.37	0.09	4.94E-155	2.11E-152	Downregulated
ENSG00000130707.18	ASS1	570.96	-1.27	0.11	1.89E-29	7.70E-28	Downregulated
ENSG00000130741.11	EIF2S3	3265.55	-1.18	0.06	2.69E-100	5.28E-98	Downregulated
ENSG00000131067.17	GGT7	810.66	-1.12	0.09	2.80E-33	1.31E-31	Downregulated
ENSG00000132182.13	NUP210	6402.1	-1.51	0.04	8.63E-279	8.71E-276	Downregulated
ENSG00000132470.14	ITGB4	46.61	-1.35	0.37	2.69E-04	1.31E-03	Downregulated
ENSG00000132938.22	MTUS2	160.72	-1.55	0.2	2.68E-14	4.52E-13	Downregulated
ENSG00000133243.10	BTBD2	1031.28	-1.6	0.09	4.95E-72	6.24E-70	Downregulated
ENSG00000134419.15	RPS15A	1302.7	-1.33	0.08	3.32E-70	4.05E-68	Downregulated
ENSG00000135318.12	NT5E	22.03	-1.53	0.55	5.28E-03	1.86E-02	Downregulated
ENSG00000135390.21	ATP5MC2	7700.41	-1.23	0.04	4.49E-209	2.89E-206	Downregulated
ENSG00000135636.16	DYSF	52.18	-1.13	0.35	1.21E-03	5.11E-03	Downregulated
ENSG00000137154.13	RPS6	10920.84	-1.15	0.04	7.77E-229	6.10E-226	Downregulated
ENSG00000137404.15	NRM	579.59	-1.1	0.11	1.28E-24	4.14E-23	Downregulated
ENSG00000137809.17	ITGA11	9.99	-1.81	0.82	2.84E-02	7.96E-02	Downregulated
ENSG00000138326.21	RPS24	4573.99	-1.35	0.05	1.55E-185	7.83E-183	Downregulated
ENSG00000138430.16	OLA1	1055.64	-1.06	0.08	1.90E-36	9.83E-35	Downregulated
ENSG00000138587.6	MNS1	48.3	-1.01	0.37	5.56E-03	1.95E-02	Downregulated
ENSG00000141756.19	FKBP10	4646.94	-1.0	0.05	1.94E-101	3.97E-99	Downregulated
ENSG00000142156.16	COL6A1	2029.43	-1.08	0.06	7.94E-69	9.36E-67	Downregulated
ENSG00000142173.16	COL6A2	1126.38	-1.38	0.08	3.40E-65	3.73E-63	Downregulated
ENSG00000142534.7	RPS11	9056.51	-1.45	0.04	0.00E+00	0.00E+00	Downregulated
ENSG00000142541.18	RPL13A	1326.28	-1.24	0.08	3.18E-55	2.79E-53	Downregulated
ENSG00000142676.14	RPL11	8389.68	-1.32	0.04	1.70E-258	1.60E-255	Downregulated
ENSG00000142694.7	EVA1B	42.59	-1.29	0.39	8.61E-04	3.76E-03	Downregulated
ENSG00000142798.20	HSPG2	810.38	-2.85	0.11	7.70E-154	3.20E-151	Downregulated
ENSG00000143162.9	CREG1	885.39	-1.1	0.09	2.24E-35	1.13E-33	Downregulated
ENSG00000143545.10	RAB13	281.16	-1.45	0.16	5.05E-20	1.27E-18	Downregulated
ENSG00000143632.15	ACTA1	58.79	-1.01	0.32	1.92E-03	7.64E-03	Downregulated
ENSG00000144713.13	RPL32	1002.27	-1.24	0.09	5.21E-43	3.35E-41	Downregulated
ENSG00000147100.11	SLC16A2	789.28	-1.07	0.09	2.48E-30	1.04E-28	Downregulated
ENSG00000147677.12	EIF3H	2835.09	-1.14	0.06	2.42E-90	4.27E-88	Downregulated
ENSG00000148730.7	EIF4EBP2	414.02	-1.01	0.13	1.30E-14	2.24E-13	Downregulated
ENSG00000148908.15	RGS10	272.01	-1.55	0.16	4.77E-22	1.37E-20	Downregulated
ENSG00000149131.17	SERPING1	43.14	-1.08	0.39	5.27E-03	1.86E-02	Downregulated
ENSG00000149273.15	RPS3	9771.89	-1.08	0.04	4.32E-188	2.35E-185	Downregulated
ENSG00000151176.8	PLBD2	1120.91	-1.2	0.08	2.53E-51	1.94E-49	Downregulated
ENSG00000152936.11	LMNTD1	36.55	-1.32	0.43	2.02E-03	7.99E-03	Downregulated
ENSG00000156508.19	EEF1A1	1056.15	-1.73	0.09	1.74E-82	2.74E-80	Downregulated
ENSG00000159640.17	ACE	47.09	-1.05	0.38	6.58E-03	2.25E-02	Downregulated
ENSG00000161016.18	RPL8	27234.61	-1.39	0.04	0.00E+00	0.00E+00	Downregulated
ENSG00000162244.12	RPL29	2039.96	-1.4	0.06	1.84E-113	4.20E-111	Downregulated
ENSG00000163453.11	IGFBP7	33.7	-1.32	0.44	2.44E-03	9.45E-03	Downregulated
ENSG00000163584.18	RPL22L1	818.87	-1.14	0.09	1.31E-35	6.68E-34	Downregulated
ENSG00000163754.18	GYG1	958.24	-1.02	0.09	3.94E-33	1.83E-31	Downregulated
ENSG00000163931.17	TKT	13153.7	-1.41	0.04	0.00E+00	0.00E+00	Downregulated
ENSG00000164687.11	FABP5	29.64	-1.53	0.48	1.38E-03	5.71E-03	Downregulated
ENSG00000166033.13	HTRA1	404.4	-1.56	0.13	1.37E-31	5.99E-30	Downregulated
ENSG00000167123.20	CERCAM	528.44	-1.07	0.11	2.04E-21	5.63E-20	Downregulated
ENSG00000167600.14	CYP2S1	101.74	-1.3	0.26	3.83E-07	2.96E-06	Downregulated
ENSG00000167658.16	EEF2	48433.54	-1.85	0.03	0.00E+00	0.00E+00	Downregulated
ENSG00000168268.11	NT5DC2	2195.59	-1.26	0.06	1.74E-95	3.23E-93	Downregulated
ENSG00000168356.13	SCN11A	7.46	2.29	1.01	2.25E-02	6.54E-02	Upregulated
ENSG00000169710.9	FASN	23941.3	-1.12	0.03	2.74E-232	2.28E-229	Downregulated
ENSG00000169919.17	GUSB	1047.86	-1.35	0.08	2.51E-60	2.48E-58	Downregulated
ENSG00000170275.15	CRTAP	1276.79	-1.86	0.08	1.47E-120	4.08E-118	Downregulated
ENSG00000170889.14	RPS9	2033.69	-1.48	0.06	5.82E-125	1.75E-122	Downregulated
ENSG00000171298.13	GAA	2581.22	-1.5	0.06	3.52E-151	1.38E-148	Downregulated
ENSG00000171551.12	ECEL1	99.21	-1.35	0.26	1.32E-07	1.08E-06	Downregulated
ENSG00000171858.18	RPS21	3547.33	-1.32	0.05	1.89E-151	7.64E-149	Downregulated
ENSG00000172487.4	OR8J1	90.74	-1.5	0.27	2.74E-08	2.50E-07	Downregulated
ENSG00000172889.16	EGFL7	426.47	-1.05	0.21	5.02E-07	3.80E-06	Downregulated
ENSG00000174080.12	CTSF	252.45	-1.04	0.16	1.06E-10	1.30E-09	Downregulated
ENSG00000175018.13	TEX36	3103.64	-1.03	0.05	1.66E-80	2.42E-78	Downregulated
ENSG00000175390.15	EIF3F	833.2	-1.39	0.09	1.70E-51	1.31E-49	Downregulated
ENSG00000177600.9	RPLP2	5089.02	-1.7	0.05	5.04E-303	5.48E-300	Downregulated
ENSG00000178403.4	NEUROG2	18.01	-1.59	0.61	9.34E-03	3.05E-02	Downregulated
ENSG00000179163.12	FUCA1	725.12	-1.02	0.1	1.69E-25	5.69E-24	Downregulated
ENSG00000180096.13	SEPTIN1	66.45	-1.22	0.31	9.12E-05	4.91E-04	Downregulated
ENSG00000180574.4	EIF2S3B	931.58	-1.27	0.09	5.89E-49	4.36E-47	Downregulated
ENSG00000180879.14	SSR4	6129.71	-1.24	0.05	2.51E-159	1.11E-156	Downregulated
ENSG00000182054.10	IDH2	1372.44	-1.04	0.07	2.47E-45	1.68E-43	Downregulated
ENSG00000182774.13	RPS17	1174.68	-1.01	0.14	5.27E-13	8.10E-12	Downregulated
ENSG00000182871.16	COL18A1	1370.02	-1.98	0.08	1.37E-135	4.40E-133	Downregulated
ENSG00000184009.13	ACTG1	43552.48	-1.09	0.03	1.59E-235	1.40E-232	Downregulated
ENSG00000184110.15	EIF3C	67.14	-1.42	0.31	5.79E-06	3.82E-05	Downregulated
ENSG00000185055.11	EFCAB10	99.94	-1.02	0.25	4.51E-05	2.57E-04	Downregulated
ENSG00000185164.15	NOMO2	227.64	-1.21	0.17	9.89E-13	1.49E-11	Downregulated
ENSG00000185624.16	P4HB	10363.63	-1.08	0.04	2.09E-189	1.18E-186	Downregulated
ENSG00000186468.13	RPS23	3272.44	-1.32	0.05	2.37E-135	7.43E-133	Downregulated
ENSG00000186501.15	TMEM222	3351.45	-1.16	0.05	8.45E-101	1.68E-98	Downregulated
ENSG00000187109.15	NAP1L1	3505.93	-1.14	0.05	8.85E-111	1.95E-108	Downregulated
ENSG00000187244.12	BCAM	250.07	-1.04	0.17	1.24E-09	1.32E-08	Downregulated
ENSG00000188157.15	AGRN	1026.98	-2.14	0.09	9.33E-120	2.49E-117	Downregulated
ENSG00000188385.13	JAKMIP3	7.4	2.3	1.01	2.32E-02	6.70E-02	Upregulated
ENSG00000188846.14	RPL14	2589.2	-1.46	0.06	8.19E-143	2.89E-140	Downregulated
ENSG00000196756.15	SNHG17	4572.8	1.02	0.05	2.01E-84	3.23E-82	Upregulated
ENSG00000196787.4	H2AC11	12007.95	-1.06	0.04	8.47E-150	3.23E-147	Downregulated
ENSG00000196961.13	AP2A1	2449.4	-1.38	0.06	2.80E-122	7.90E-120	Downregulated
ENSG00000197111.16	PCBP2	2110.66	-1.18	0.06	3.65E-83	5.80E-81	Downregulated
ENSG00000197585.10	ENSG00000197585	86.64	-1.32	0.28	2.04E-06	1.42E-05	Downregulated
ENSG00000197756.10	RPL37A	4406.61	-1.38	0.05	9.53E-163	4.34E-160	Downregulated
ENSG00000198673.11	TAFA2	227.2	-1.45	0.17	2.49E-17	5.31E-16	Downregulated
ENSG00000198755.11	RPL10A	2586.19	-1.01	0.06	1.01E-70	1.24E-68	Downregulated
ENSG00000198816.7	ZNF358	221.72	-1.59	0.18	3.19E-18	7.18E-17	Downregulated
ENSG00000203907.10	OOEP	244.39	-1.0	0.16	9.90E-10	1.07E-08	Downregulated
ENSG00000204390.10	HSPA1L	87.63	-1.39	0.27	4.02E-07	3.09E-06	Downregulated
ENSG00000204628.12	RACK1	40145.87	-1.2	0.03	2.48E-307	2.92E-304	Downregulated
ENSG00000205846.4	CLEC6A	65.81	-1.34	0.32	2.30E-05	1.37E-04	Downregulated
ENSG00000213585.11	VDAC1	1209.53	-1.17	0.08	9.47E-53	7.69E-51	Downregulated
ENSG00000213614.11	HEXA	2299.18	-1.05	0.06	2.99E-71	3.71E-69	Downregulated
ENSG00000221983.8	UBA52	5047.17	-1.4	0.05	6.99E-208	4.30E-205	Downregulated
ENSG00000223598.1	ENSG00000223598	30.84	-1.71	0.48	3.38E-04	1.61E-03	Downregulated
ENSG00000224063.6	CALCRL-AS1	60.63	-1.46	0.34	1.34E-05	8.37E-05	Downregulated
ENSG00000225914.5	TSBP1-AS1	18.71	-1.38	0.59	1.86E-02	5.56E-02	Downregulated
ENSG00000226784.3	PGAM4	64.77	-1.08	0.31	4.99E-04	2.30E-03	Downregulated
ENSG00000227240.2	ENSG00000227240	96.38	-1.98	0.28	1.07E-12	1.60E-11	Downregulated
ENSG00000231090.2	MIR4422HG	83.0	-1.1	0.29	1.60E-04	8.18E-04	Downregulated
ENSG00000231236.2	ENSG00000231236	97.78	-1.29	0.26	5.72E-07	4.29E-06	Downregulated
ENSG00000231427.6	LINC01445	78.38	-1.43	0.29	1.05E-06	7.58E-06	Downregulated
ENSG00000231718.1	LINC02789	76.48	-1.65	0.31	1.07E-07	8.89E-07	Downregulated
ENSG00000232712.6	KIZ-AS1	9.76	-1.99	0.86	2.08E-02	6.11E-02	Downregulated
ENSG00000233087.8	RAB6D	26.57	1.54	0.51	2.85E-03	1.08E-02	Upregulated
ENSG00000233420.2	ENSG00000233420	121.01	-1.57	0.24	4.26E-11	5.40E-10	Downregulated
ENSG00000235979.9	ENSG00000235979	381.3	-1.6	0.14	4.41E-31	1.89E-29	Downregulated
ENSG00000236830.8	CBR3-AS1	24.88	-1.38	0.51	7.14E-03	2.41E-02	Downregulated
ENSG00000240038.7	AMY2B	37.18	-1.04	0.41	1.22E-02	3.88E-02	Downregulated
ENSG00000244509.4	APOBEC3C	19.1	-1.34	0.61	2.68E-02	7.55E-02	Downregulated
ENSG00000249856.1	ENSG00000249856	6.03	-2.34	1.12	3.62E-02	9.67E-02	Downregulated
ENSG00000251600.8	ENSG00000251600	18.12	-1.34	0.61	2.89E-02	8.07E-02	Downregulated
ENSG00000253626.4	EIF5AL1	724.43	1.18	0.1	1.20E-33	5.66E-32	Upregulated
ENSG00000254266.6	PKIA-AS1	8.97	-2.06	0.9	2.19E-02	6.37E-02	Downregulated
ENSG00000254772.10	EEF1G	1870.28	-1.38	0.07	4.59E-98	8.65E-96	Downregulated
ENSG00000257407.1	ENSG00000257407	36.69	-1.34	0.42	1.32E-03	5.52E-03	Downregulated
ENSG00000257443.2	LRIG3-DT	8.51	-1.98	0.92	3.03E-02	8.39E-02	Downregulated
ENSG00000257595.3	LINC02356	86.96	-1.62	0.28	4.68E-09	4.69E-08	Downregulated
ENSG00000259240.1	MIR4713HG	17.03	1.37	0.62	2.77E-02	7.79E-02	Upregulated
ENSG00000259843.2	HEATR3-AS1	122.86	-1.44	0.23	8.86E-10	9.64E-09	Downregulated
ENSG00000260983.2	ENSG00000260983	73.14	-1.2	0.32	1.59E-04	8.17E-04	Downregulated
ENSG00000270379.6	HEATR9	41.59	-1.18	0.42	4.64E-03	1.66E-02	Downregulated
ENSG00000277586.4	NEFL	1021.97	-1.03	0.08	1.24E-35	6.32E-34	Downregulated
ENSG00000280560.3	LINC01374	259.2	-1.17	0.16	4.03E-13	6.27E-12	Downregulated
ENSG00000286377.1	ENSG00000286377	54.46	-1.48	0.35	2.18E-05	1.31E-04	Downregulated
ENSG00000288920.1	RPSAP58	123.66	-1.21	0.24	2.58E-07	2.03E-06	Downregulated

RPF Gene Enrichment

The GO term and KEGG pathway enrichment analyses show which functional gene categories and pathways are enriched in up- and downregulated genes from the volcano plot above. GO and KEGG analyses were performed with clusterProfiler's enrichGO and enrichKEGG functions. Within each domain are boxes for each gene ontology or KEGG term, and within each term are the contributing genes. The color of the gene box is the log₂ fold change between the two sample conditions while the size of the gene box is based off the -log₁₀(adjusted p-value) for the comparison. The color and size of the term boxes are based off the sum of all contributing genes. You can click on individual GO categories and subcategories to zoom and view their results in more detail. Clicking on the "Analysis" heading will restore the plot to its original appearance. For each gene box, the hover will show the adjusted p-value for the performed comparison and log₂ fold change of the listed gene. For each term, the hover will show the adjusted p-value for the enrichment analysis and the average fold change of all genes included in the box. Significance and fold changes are not provided for the domains.

Two libraries were generated from each sample: a ribosome protected footprint (RPF) library and an RNA-Seq library. This tab shows the differences in ribosome occupancy (RO, also called translational efficiency or TE) between two sample groups, where RO is defined as the RPF counts over the RNA-Seq library counts for each gene. Please refer to the per sample reports for tables of RO values per gene for each individual sample. The comparison for this analysis is Treated over Untreated. All analyses on this tab were performed on a whole gene level.

RO Volcano Plot

The plot below shows a comparison between fold change and significance in ribosome occupancy between Treated and Untreated samples. The x-axis shows the fold change ("log₂(fold change)") and the x-axis shows significance("-log₁₀(adjusted p-value)"). Red (increased in Treated) and teal (decreased in Treated) dots represent genes that are significantly different between conditions. Gray dots represent genes that are not significant. Hovering your mouse over the volcano plot below will show the gene name, Ensembl gene ID, -log₁₀(adjusted p-value), and log₂(fold change) for each point.

Differential RO Table

We used a differential expression analysis tool called DESeq2 to compare Treated and Untreated samples. The table below lists the average normalized expression in the RPF and RNA-Seq libraries, as well as the fold change differences in ribosome occupancy (RO). The significance of the RO difference was determined by extending DESeq2 models to include RO fold change as an interaction between the experimental condition and the library type. The adjusted p-values of these interactions were used to identify genes with significant RO fold change between conditions. Genes with a RO log₂(fold change) > 1 and an adjusted p-value < 0.1 were defined as having upregulated RO. Genes with a RO log₂(fold change) < -1 and an adjusted p-value < 0.1 were defined as having downregulated RO. Only genes annotated as protein coding or lncRNA are included in the table. Multimapping reads were removed before the analysis, which may reduce estimates for genes with high pseudogenization or duplication events.

The following columns are included in the table:

Ensembl ID: Ensembl's unique identifier and version of a gene
Gene name: common name for the gene.
RPF baseMean: average DESeq2-normalized counts across all samples and all conditions in the RPF libraries
RNA-Seq baseMean: average DESeq2-normalized counts across all samples and all conditions in the RNA-Seq libraries
log₂(fold change): log₂-transformed ratio of RO between the two conditions
log₂(SE): log₂-transformed standard error
P-value: unadjusted measure of significance
Adjusted p-value: false discovery rate (FDR) adjusted significance
Up/downregulated: classification of expression change based on the significance and fold change

A copy of the table can be downloaded by clicking the button of the desired format (CSV, Excel or PDF)

Ensembl ID	Gene name	RPF baseMean	RNA-Seq baseMean	log₂(fold change)	log₂(SE)	P-value	Adjusted p-value	Up/downregulated
ENSG00000005022.6	SLC25A5	15767.99	25540.59	-1.57	0.04	0.00E+00	0.00E+00	Downregulated
ENSG00000005206.17	SPPL2B	519.23	2210.03	-1.15	0.11	1.05E-26	4.85E-25	Downregulated
ENSG00000007952.18	NOX1	445.69	21.53	-1.03	0.36	4.41E-03	1.67E-02	Downregulated
ENSG00000008988.11	RPS20	693.25	16209.14	-1.75	0.08	4.95E-102	1.21E-99	Downregulated
ENSG00000009307.17	CSDE1	10876.56	41535.6	-1.1	0.04	1.06E-135	4.14E-133	Downregulated
ENSG00000011028.14	MRC2	443.39	1684.73	-1.34	0.12	1.03E-28	5.29E-27	Downregulated
ENSG00000026025.16	VIM	21849.69	37001.86	-1.95	0.04	0.00E+00	0.00E+00	Downregulated
ENSG00000030582.18	GRN	6762.64	9163.74	-1.07	0.06	2.40E-80	4.41E-78	Downregulated
ENSG00000037042.9	TUBG2	186.72	331.16	-1.02	0.21	8.08E-07	6.95E-06	Downregulated
ENSG00000050555.19	LAMC3	221.58	967.67	-1.34	0.16	1.60E-17	4.38E-16	Downregulated
ENSG00000060138.13	YBX3	3519.84	10749.47	-1.29	0.06	4.58E-120	1.41E-117	Downregulated
ENSG00000062582.14	MRPS24	1752.56	3613.78	-1.04	0.07	6.41E-46	5.70E-44	Downregulated
ENSG00000063177.13	RPL18	8962.39	37218.15	-1.39	0.06	3.81E-132	1.42E-129	Downregulated
ENSG00000064666.15	CNN2	441.0	1535.7	-1.37	0.12	1.91E-29	1.02E-27	Downregulated
ENSG00000065150.21	IPO5	9578.8	34010.38	-1.24	0.04	1.04E-178	7.01E-176	Downregulated
ENSG00000065427.15	KARS1	4534.75	7711.71	-1.08	0.05	5.27E-89	1.10E-86	Downregulated
ENSG00000065978.19	YBX1	2029.87	16543.42	-1.56	0.06	1.23E-144	5.80E-142	Downregulated
ENSG00000070756.17	PABPC1	3828.69	22946.36	-3.19	0.07	0.00E+00	0.00E+00	Downregulated
ENSG00000070915.10	SLC12A3	23.21	57.48	-2.26	0.57	8.37E-05	5.01E-04	Downregulated
ENSG00000071082.11	RPL31	1681.15	27627.07	-1.73	0.06	2.14E-171	1.32E-168	Downregulated
ENSG00000074181.9	NOTCH3	1162.44	5034.18	-1.44	0.08	5.93E-67	8.37E-65	Downregulated
ENSG00000078053.17	AMPH	309.12	840.18	-1.11	0.15	5.06E-14	1.04E-12	Downregulated
ENSG00000079739.17	PGM1	3214.18	3341.99	-1.32	0.07	3.04E-76	5.31E-74	Downregulated
ENSG00000083444.17	PLOD1	2493.85	5664.77	-1.02	0.06	3.79E-59	4.74E-57	Downregulated
ENSG00000083845.9	RPS5	5307.49	15880.77	-1.86	0.06	1.07E-184	7.94E-182	Downregulated
ENSG00000089157.16	RPLP0	1420.84	27604.25	-1.96	0.07	4.13E-193	3.43E-190	Downregulated
ENSG00000089327.15	FXYD5	605.87	326.12	-1.41	0.16	4.27E-19	1.30E-17	Downregulated
ENSG00000089351.15	GRAMD1A	787.12	3250.5	-1.16	0.09	9.39E-37	6.57E-35	Downregulated
ENSG00000092445.12	TYRO3	306.87	2773.77	-1.04	0.12	2.84E-18	8.12E-17	Downregulated
ENSG00000095585.18	BLNK	525.67	61.02	-1.07	0.48	2.63E-02	7.43E-02	Downregulated
ENSG00000100258.18	LMF2	1219.01	3196.65	-1.15	0.09	9.14E-40	6.87E-38	Downregulated
ENSG00000100979.15	PLTP	1937.65	1352.72	-1.07	0.09	1.77E-32	1.05E-30	Downregulated
ENSG00000101115.13	SALL4	15.06	54.41	-1.39	0.6	2.01E-02	5.95E-02	Downregulated
ENSG00000101210.13	EEF1A2	2576.73	3504.41	-1.15	0.07	1.76E-57	2.09E-55	Downregulated
ENSG00000101444.13	AHCY	6402.39	19356.3	-1.62	0.05	1.37E-258	3.24E-255	Downregulated
ENSG00000101911.13	PRPS2	2295.79	5349.74	-1.27	0.06	1.09E-87	2.22E-85	Downregulated
ENSG00000102030.16	NAA10	2457.38	5864.2	-1.11	0.06	1.55E-70	2.35E-68	Downregulated
ENSG00000102882.12	MAPK3	2181.6	3720.79	-1.0	0.07	8.91E-50	8.69E-48	Downregulated
ENSG00000103226.19	NOMO3	118.42	385.07	-1.16	0.22	1.29E-07	1.27E-06	Downregulated
ENSG00000103257.9	SLC7A5	4714.69	23564.67	-1.17	0.05	8.14E-112	2.30E-109	Downregulated
ENSG00000103512.16	NOMO1	478.99	2069.68	-1.44	0.11	1.68E-40	1.29E-38	Downregulated
ENSG00000104529.19	EEF1D	2369.02	12291.52	-1.3	0.06	2.35E-110	6.39E-108	Downregulated
ENSG00000104774.13	MAN2B1	700.73	3267.34	-1.26	0.1	1.14E-39	8.55E-38	Downregulated
ENSG00000104805.16	NUCB1	2349.01	4210.73	-1.03	0.07	4.04E-54	4.36E-52	Downregulated
ENSG00000104853.16	CLPTM1	2267.38	4856.59	-2.11	0.07	5.60E-195	5.28E-192	Downregulated
ENSG00000104863.12	LIN7B	34.48	158.25	-1.27	0.37	6.68E-04	3.22E-03	Downregulated
ENSG00000105193.9	RPS16	6212.19	23986.75	-1.38	0.05	9.18E-175	5.90E-172	Downregulated
ENSG00000105220.17	GPI	15923.77	21990.9	-1.11	0.04	4.16E-147	2.03E-144	Downregulated
ENSG00000105372.8	RPS19	4108.77	53387.3	-1.54	0.05	2.61E-249	5.26E-246	Downregulated
ENSG00000105409.19	ATP1A3	1712.31	2338.45	-1.12	0.08	1.43E-44	1.23E-42	Downregulated
ENSG00000105613.10	MAST1	255.8	644.29	-1.19	0.16	1.11E-13	2.19E-12	Downregulated
ENSG00000105726.17	ATP13A1	1833.11	3612.85	-1.24	0.08	9.48E-59	1.18E-56	Downregulated
ENSG00000105750.15	ZNF85	17.95	59.29	1.19	0.55	3.16E-02	8.64E-02	Upregulated
ENSG00000106554.13	CHCHD3	2869.09	37697.68	-1.28	0.05	9.64E-144	4.39E-141	Downregulated
ENSG00000107331.18	ABCA2	505.21	3521.37	-1.13	0.1	1.76E-28	8.93E-27	Downregulated
ENSG00000108107.15	RPL28	2701.12	3857.21	-1.86	0.08	7.66E-130	2.58E-127	Downregulated
ENSG00000109475.17	RPL34	1049.96	11351.07	-1.16	0.16	1.80E-13	3.51E-12	Downregulated
ENSG00000109736.15	MFSD10	909.03	2512.76	-1.03	0.09	9.70E-31	5.42E-29	Downregulated
ENSG00000109971.14	HSPA8	12607.21	24144.88	-1.81	0.05	2.17E-245	3.40E-242	Downregulated
ENSG00000110700.7	RPS13	5770.42	13991.37	-1.08	0.05	4.10E-111	1.14E-108	Downregulated
ENSG00000111640.15	GAPDH	18332.79	60144.21	-2.21	0.04	0.00E+00	0.00E+00	Downregulated
ENSG00000113504.21	SLC12A7	619.07	1644.06	-1.17	0.11	2.57E-27	1.24E-25	Downregulated
ENSG00000114391.13	RPL24	3787.34	12611.47	-1.09	0.06	1.50E-80	2.83E-78	Downregulated
ENSG00000115380.20	EFEMP1	121.32	140.21	-1.47	0.28	2.16E-07	2.05E-06	Downregulated
ENSG00000116251.11	RPL22	295.95	6581.25	-1.32	0.11	2.46E-33	1.50E-31	Downregulated
ENSG00000116852.15	KIF21B	90.78	638.26	-1.13	0.21	1.18E-07	1.16E-06	Downregulated
ENSG00000116962.15	NID1	7915.94	4966.17	-1.19	0.05	3.55E-104	8.81E-102	Downregulated
ENSG00000118816.11	CCNI	2795.39	13964.69	-1.34	0.06	2.12E-130	7.70E-128	Downregulated
ENSG00000123143.13	PKN1	1605.97	6444.86	-1.09	0.07	3.53E-58	4.30E-56	Downregulated
ENSG00000124155.19	PIGT	1648.45	3402.9	-1.12	0.08	1.27E-47	1.18E-45	Downregulated
ENSG00000124721.18	DNAH8	22.12	25.65	1.89	0.65	3.69E-03	1.43E-02	Upregulated
ENSG00000125743.11	SNRPD2	6913.68	11660.02	-1.2	0.05	2.50E-130	8.85E-128	Downregulated
ENSG00000125912.11	NCLN	1844.15	8915.02	-1.14	0.06	8.39E-75	1.41E-72	Downregulated
ENSG00000127022.16	CANX	19.08	378.42	-1.55	0.42	2.66E-04	1.41E-03	Downregulated
ENSG00000129946.11	SHC2	17.83	191.59	-2.03	0.5	5.69E-05	3.52E-04	Downregulated
ENSG00000130005.13	GAMT	694.18	1671.06	-1.22	0.11	7.20E-31	4.05E-29	Downregulated
ENSG00000130203.10	APOE	404.69	471.25	-1.12	0.16	1.30E-12	2.35E-11	Downregulated
ENSG00000130702.15	LAMA5	1122.12	3547.06	-2.23	0.1	2.36E-101	5.64E-99	Downregulated
ENSG00000130741.11	EIF2S3	3265.55	14750.34	-1.2	0.06	1.10E-99	2.59E-97	Downregulated
ENSG00000131067.17	GGT7	810.66	2496.75	-1.06	0.09	2.70E-29	1.43E-27	Downregulated
ENSG00000132182.13	NUP210	6402.1	18103.29	-1.49	0.05	5.35E-201	5.81E-198	Downregulated
ENSG00000132470.14	ITGB4	46.61	97.78	-1.22	0.39	1.90E-03	8.07E-03	Downregulated
ENSG00000132622.11	HSPA12B	8.72	17.57	2.57	0.94	6.28E-03	2.24E-02	Upregulated
ENSG00000132938.22	MTUS2	160.72	74.7	-1.87	0.31	9.04E-10	1.19E-08	Downregulated
ENSG00000133243.10	BTBD2	1031.28	7551.91	-1.49	0.08	1.62E-77	2.91E-75	Downregulated
ENSG00000134243.12	SORT1	1665.91	7312.62	-1.01	0.07	7.79E-54	8.28E-52	Downregulated
ENSG00000134419.15	RPS15A	1302.7	21125.17	-1.36	0.06	2.66E-105	6.70E-103	Downregulated
ENSG00000135114.14	OASL	8.09	7.83	-3.09	1.28	1.59E-02	4.88E-02	Downregulated
ENSG00000135318.12	NT5E	22.03	36.84	-1.39	0.61	2.39E-02	6.87E-02	Downregulated
ENSG00000135390.21	ATP5MC2	7700.41	3330.19	-1.42	0.11	2.22E-36	1.54E-34	Downregulated
ENSG00000135519.8	KCNH3	14.11	130.56	1.07	0.51	3.65E-02	9.74E-02	Upregulated
ENSG00000135525.19	MAP7	618.26	953.17	-1.04	0.12	3.16E-18	9.01E-17	Downregulated
ENSG00000137154.13	RPS6	10920.84	73962.34	-1.16	0.04	3.95E-148	1.99E-145	Downregulated
ENSG00000137818.12	RPLP1	3743.15	19348.74	-1.12	0.11	1.18E-22	4.37E-21	Downregulated
ENSG00000137955.16	RABGGTB	3797.06	4723.91	-1.1	0.37	2.72E-03	1.10E-02	Downregulated
ENSG00000138326.21	RPS24	4573.99	30286.86	-1.38	0.05	5.47E-143	2.42E-140	Downregulated
ENSG00000138430.16	OLA1	1055.64	5936.5	-1.1	0.08	2.90E-47	2.67E-45	Downregulated
ENSG00000138587.6	MNS1	48.3	110.67	-1.24	0.38	9.69E-04	4.46E-03	Downregulated
ENSG00000142156.16	COL6A1	2029.43	4374.82	-1.1	0.07	8.15E-57	9.60E-55	Downregulated
ENSG00000142173.16	COL6A2	1126.38	2585.99	-1.34	0.09	1.34E-52	1.40E-50	Downregulated
ENSG00000142534.7	RPS11	9056.51	24906.07	-1.55	0.05	9.82E-194	8.68E-191	Downregulated
ENSG00000142541.18	RPL13A	1326.28	22369.08	-1.21	0.06	1.74E-80	3.24E-78	Downregulated
ENSG00000142676.14	RPL11	8389.68	28519.57	-1.37	0.05	1.11E-185	8.74E-183	Downregulated
ENSG00000142694.7	EVA1B	42.59	199.33	-1.24	0.34	2.54E-04	1.36E-03	Downregulated
ENSG00000142798.20	HSPG2	810.38	1541.39	-2.75	0.12	2.57E-113	7.42E-111	Downregulated
ENSG00000143162.9	CREG1	885.39	4228.43	-1.02	0.08	1.31E-35	8.71E-34	Downregulated
ENSG00000143545.10	RAB13	281.16	650.24	-1.3	0.17	4.86E-15	1.08E-13	Downregulated
ENSG00000144713.13	RPL32	1002.27	24567.7	-1.27	0.07	1.61E-74	2.67E-72	Downregulated
ENSG00000145592.14	RPL37	3597.01	18465.23	-1.04	0.05	1.41E-80	2.69E-78	Downregulated
ENSG00000147100.11	SLC16A2	789.28	1376.47	-1.04	0.1	2.10E-23	8.10E-22	Downregulated
ENSG00000147408.16	CSGALNACT1	29.61	55.07	1.33	0.5	7.30E-03	2.54E-02	Upregulated
ENSG00000147677.12	EIF3H	2835.09	6959.06	-1.23	0.07	1.22E-73	1.98E-71	Downregulated
ENSG00000148908.15	RGS10	272.01	1633.75	-1.47	0.14	2.40E-25	1.02E-23	Downregulated
ENSG00000149131.17	SERPING1	43.14	22.92	-1.39	0.57	1.40E-02	4.40E-02	Downregulated
ENSG00000149273.15	RPS3	9771.89	44619.97	-1.14	0.05	7.02E-139	2.92E-136	Downregulated
ENSG00000150990.9	DHX37	1549.0	4721.29	-1.04	0.07	4.18E-50	4.13E-48	Downregulated
ENSG00000151176.8	PLBD2	1120.91	863.95	-1.23	0.11	4.33E-30	2.39E-28	Downregulated
ENSG00000152936.11	LMNTD1	36.55	94.35	-1.28	0.45	4.36E-03	1.65E-02	Downregulated
ENSG00000156508.19	EEF1A1	1056.15	21783.24	-1.71	0.07	6.26E-130	2.16E-127	Downregulated
ENSG00000158246.8	TENT5B	48.32	64.17	1.05	0.44	1.80E-02	5.44E-02	Upregulated
ENSG00000159905.15	ZNF221	70.96	87.89	1.05	0.36	3.99E-03	1.53E-02	Upregulated
ENSG00000160161.9	CILP2	630.63	1304.98	-1.13	0.12	1.55E-22	5.68E-21	Downregulated
ENSG00000161016.18	RPL8	27234.61	68344.47	-1.47	0.04	4.40E-243	6.21E-240	Downregulated
ENSG00000161970.15	RPL26	2189.18	11883.86	-1.08	0.07	3.52E-49	3.36E-47	Downregulated
ENSG00000162244.12	RPL29	2039.96	17977.39	-1.54	0.06	2.18E-155	1.19E-152	Downregulated
ENSG00000163453.11	IGFBP7	33.7	73.49	-1.01	0.46	2.75E-02	7.70E-02	Downregulated
ENSG00000163584.18	RPL22L1	818.87	2710.91	-1.4	0.09	5.76E-55	6.46E-53	Downregulated
ENSG00000163754.18	GYG1	958.24	2380.57	-1.1	0.09	9.14E-35	5.95E-33	Downregulated
ENSG00000163931.17	TKT	13153.7	25000.21	-1.48	0.04	3.71E-248	6.55E-245	Downregulated
ENSG00000164304.16	CAGE1	1528.85	2255.99	-1.0	0.08	8.69E-35	5.68E-33	Downregulated
ENSG00000164687.11	FABP5	29.64	472.69	-1.62	0.35	3.01E-06	2.35E-05	Downregulated
ENSG00000164916.11	FOXK1	1557.7	13365.88	-1.08	0.06	3.26E-62	4.22E-60	Downregulated
ENSG00000165246.15	NLGN4Y	64.3	34.95	1.0	0.46	2.75E-02	7.71E-02	Upregulated
ENSG00000165863.17	C10orf82	23.06	59.99	-1.13	0.53	3.30E-02	8.95E-02	Downregulated
ENSG00000166033.13	HTRA1	404.4	1012.74	-1.28	0.14	2.36E-20	7.66E-19	Downregulated
ENSG00000167600.14	CYP2S1	101.74	146.66	-1.52	0.3	3.77E-07	3.41E-06	Downregulated
ENSG00000167658.16	EEF2	48433.54	278130.39	-1.82	0.04	0.00E+00	0.00E+00	Downregulated
ENSG00000167779.9	IGFBP6	25.54	38.37	-1.18	0.56	3.54E-02	9.49E-02	Downregulated
ENSG00000168268.11	NT5DC2	2195.59	11664.66	-1.28	0.06	5.45E-106	1.40E-103	Downregulated
ENSG00000168356.13	SCN11A	7.46	58.3	2.34	0.85	5.73E-03	2.07E-02	Upregulated
ENSG00000169252.6	ADRB2	26.62	40.37	1.38	0.56	1.30E-02	4.14E-02	Upregulated
ENSG00000169710.9	FASN	23941.3	56069.4	-1.5	0.05	5.88E-168	3.32E-165	Downregulated
ENSG00000169727.13	GPS1	4930.73	10080.02	-1.06	0.05	2.26E-93	4.99E-91	Downregulated
ENSG00000169919.17	GUSB	1047.86	2563.52	-1.32	0.09	6.60E-52	6.71E-50	Downregulated
ENSG00000170275.15	CRTAP	1276.79	10492.7	-1.77	0.07	1.11E-140	4.77E-138	Downregulated
ENSG00000170889.14	RPS9	2033.69	23825.82	-1.54	0.06	1.17E-170	6.91E-168	Downregulated
ENSG00000171298.13	GAA	2581.22	6283.4	-1.48	0.06	3.46E-119	1.04E-116	Downregulated
ENSG00000171408.14	PDE7B	21.33	43.81	1.41	0.58	1.51E-02	4.68E-02	Upregulated
ENSG00000171551.12	ECEL1	99.21	537.63	-1.21	0.22	3.40E-08	3.66E-07	Downregulated
ENSG00000171858.18	RPS21	3547.33	14803.38	-1.43	0.06	5.44E-135	2.08E-132	Downregulated
ENSG00000172421.10	EFCAB3	278.09	566.76	-1.11	0.16	7.59E-12	1.28E-10	Downregulated
ENSG00000172487.4	OR8J1	90.74	60.52	-1.64	0.37	8.82E-06	6.33E-05	Downregulated
ENSG00000172733.12	PURG	35.33	310.55	1.23	0.34	2.61E-04	1.39E-03	Upregulated
ENSG00000172889.16	EGFL7	426.47	1014.1	-1.06	0.14	1.31E-13	2.58E-12	Downregulated
ENSG00000173638.19	SLC19A1	2266.48	6945.38	-1.03	0.07	2.58E-55	2.92E-53	Downregulated
ENSG00000175018.13	TEX36	3103.64	470.03	-1.17	0.1	2.09E-31	1.21E-29	Downregulated
ENSG00000175265.19	GOLGA8A	8.22	259.76	1.62	0.64	1.06E-02	3.48E-02	Upregulated
ENSG00000175390.15	EIF3F	833.2	2696.06	-1.49	0.09	1.10E-58	1.35E-56	Downregulated
ENSG00000177600.9	RPLP2	5089.02	20369.39	-1.86	0.06	9.43E-203	1.11E-199	Downregulated
ENSG00000179148.10	ALOXE3	49.56	64.83	-1.07	0.42	9.68E-03	3.24E-02	Downregulated
ENSG00000180574.4	EIF2S3B	931.58	3439.25	-1.26	0.09	5.32E-45	4.64E-43	Downregulated
ENSG00000180879.14	SSR4	6129.71	9308.91	-1.24	0.06	8.95E-107	2.39E-104	Downregulated
ENSG00000181163.14	NPM1	3264.07	22829.57	-1.04	0.05	1.15E-98	2.65E-96	Downregulated
ENSG00000182379.10	NXPH4	448.89	421.36	-1.07	0.15	1.92E-12	3.42E-11	Downregulated
ENSG00000182774.13	RPS17	1174.68	17441.19	-1.09	0.14	1.51E-14	3.19E-13	Downregulated
ENSG00000182871.16	COL18A1	1370.02	6159.62	-1.99	0.08	2.04E-136	8.23E-134	Downregulated
ENSG00000182979.18	MTA1	2150.05	10102.19	-1.03	0.06	3.02E-59	3.81E-57	Downregulated
ENSG00000184009.13	ACTG1	43552.48	105957.4	-1.2	0.04	3.43E-182	2.42E-179	Downregulated
ENSG00000184110.15	EIF3C	67.14	464.29	-1.35	0.26	1.60E-07	1.54E-06	Downregulated
ENSG00000185055.11	EFCAB10	99.94	3207.9	-1.14	0.17	4.43E-11	6.83E-10	Downregulated
ENSG00000185164.15	NOMO2	227.64	773.11	-1.2	0.16	9.06E-14	1.81E-12	Downregulated
ENSG00000185624.16	P4HB	10363.63	22672.53	-1.07	0.04	1.59E-128	5.23E-126	Downregulated
ENSG00000186468.13	RPS23	3272.44	14755.15	-1.44	0.06	1.02E-117	3.00E-115	Downregulated
ENSG00000186501.15	TMEM222	3351.45	3735.91	-1.3	0.07	3.64E-73	5.85E-71	Downregulated
ENSG00000186868.17	MAPT	483.96	1344.14	-1.05	0.12	1.87E-19	5.79E-18	Downregulated
ENSG00000187109.15	NAP1L1	3505.93	17854.58	-1.19	0.06	1.97E-92	4.22E-90	Downregulated
ENSG00000187244.12	BCAM	250.07	351.77	-1.12	0.2	4.72E-08	4.98E-07	Downregulated
ENSG00000188157.15	AGRN	1026.98	4325.16	-2.2	0.09	7.12E-126	2.24E-123	Downregulated
ENSG00000188385.13	JAKMIP3	7.4	29.05	2.12	0.95	2.61E-02	7.39E-02	Upregulated
ENSG00000188846.14	RPL14	2589.2	18874.14	-1.48	0.06	4.26E-155	2.23E-152	Downregulated
ENSG00000196961.13	AP2A1	2449.4	6373.73	-1.43	0.07	1.84E-94	4.12E-92	Downregulated
ENSG00000197111.16	PCBP2	2110.66	2562.99	-1.24	0.07	1.38E-61	1.77E-59	Downregulated
ENSG00000197585.10	ENSG00000197585	86.64	109.75	-1.42	0.33	1.49E-05	1.03E-04	Downregulated
ENSG00000197756.10	RPL37A	4406.61	15869.43	-1.51	0.11	5.71E-41	4.53E-39	Downregulated
ENSG00000198673.11	TAFA2	227.2	809.8	-1.52	0.16	5.58E-21	1.87E-19	Downregulated
ENSG00000198755.11	RPL10A	2586.19	15375.4	-1.12	0.06	3.00E-83	5.89E-81	Downregulated
ENSG00000198816.7	ZNF358	221.72	1120.04	-1.67	0.16	1.76E-25	7.57E-24	Downregulated
ENSG00000203907.10	OOEP	244.39	17358.24	-1.04	0.11	1.04E-21	3.64E-20	Downregulated
ENSG00000204628.12	RACK1	40145.87	104029.24	-1.23	0.04	3.15E-214	4.05E-211	Downregulated
ENSG00000213585.11	VDAC1	1209.53	7252.47	-1.31	0.07	2.38E-78	4.32E-76	Downregulated
ENSG00000216490.4	IFI30	1018.63	1077.01	-1.05	0.11	5.46E-22	1.95E-20	Downregulated
ENSG00000221983.8	UBA52	5047.17	22937.98	-1.45	0.05	1.26E-199	1.27E-196	Downregulated
ENSG00000223561.8	LINC03007	43.31	271.47	-1.04	0.31	8.82E-04	4.12E-03	Downregulated
ENSG00000223598.1	ENSG00000223598	30.84	496.67	-1.76	0.35	4.28E-07	3.84E-06	Downregulated
ENSG00000224063.6	CALCRL-AS1	60.63	45.54	-1.43	0.47	2.16E-03	9.05E-03	Downregulated
ENSG00000225697.13	SLC26A6	1183.32	1807.23	-1.01	0.09	1.10E-27	5.42E-26	Downregulated
ENSG00000225806.8	ENSG00000225806	6.92	169.98	1.85	0.72	1.02E-02	3.37E-02	Upregulated
ENSG00000226784.3	PGAM4	64.77	22.76	-1.42	0.51	5.39E-03	1.97E-02	Downregulated
ENSG00000227240.2	ENSG00000227240	96.38	54.01	-1.84	0.39	2.58E-06	2.04E-05	Downregulated
ENSG00000228412.9	LNC-LBCS	116.65	31.21	-1.09	0.41	7.62E-03	2.64E-02	Downregulated
ENSG00000231090.2	MIR4422HG	83.0	46.87	-1.02	0.42	1.58E-02	4.87E-02	Downregulated
ENSG00000231236.2	ENSG00000231236	97.78	53.88	-1.46	0.38	1.25E-04	7.18E-04	Downregulated
ENSG00000231427.6	LINC01445	78.38	112.85	-1.25	0.34	2.01E-04	1.10E-03	Downregulated
ENSG00000231718.1	LINC02789	76.48	9.6	-1.79	0.64	5.05E-03	1.86E-02	Downregulated
ENSG00000232019.1	ENSG00000232019	110.76	225.32	-1.07	0.25	2.20E-05	1.46E-04	Downregulated
ENSG00000232712.6	KIZ-AS1	9.76	1305.94	-1.97	0.58	7.18E-04	3.44E-03	Downregulated
ENSG00000233087.8	RAB6D	26.57	106.08	1.65	0.48	6.75E-04	3.25E-03	Upregulated
ENSG00000233420.2	ENSG00000233420	121.01	16.47	-1.92	0.49	9.67E-05	5.69E-04	Downregulated
ENSG00000233635.2	ENSG00000233635	44.24	10.7	1.96	0.69	4.36E-03	1.65E-02	Upregulated
ENSG00000234390.4	USP27X-DT	12.8	69.24	1.46	0.61	1.62E-02	4.97E-02	Upregulated
ENSG00000235979.9	ENSG00000235979	381.3	21873.64	-1.62	0.1	3.85E-63	5.03E-61	Downregulated
ENSG00000236230.2	ENSG00000236230	10.23	8.2	2.24	1.05	3.28E-02	8.92E-02	Upregulated
ENSG00000236830.8	CBR3-AS1	24.88	88.01	-1.26	0.48	8.47E-03	2.89E-02	Downregulated
ENSG00000237250.3	ENSG00000237250	24.32	19.19	-1.47	0.69	3.35E-02	9.07E-02	Downregulated
ENSG00000238083.9	LRRC37A2	12.76	112.97	-1.14	0.54	3.30E-02	8.95E-02	Downregulated
ENSG00000240038.7	AMY2B	37.18	408.8	-1.21	0.31	1.10E-04	6.40E-04	Downregulated
ENSG00000242220.9	TCP10L	43.21	53.78	1.15	0.47	1.50E-02	4.65E-02	Upregulated
ENSG00000244038.11	DDOST	7917.92	10530.89	-1.02	0.05	7.57E-95	1.73E-92	Downregulated
ENSG00000244184.1	PELP1-DT	20.46	87.91	-1.07	0.49	2.83E-02	7.89E-02	Downregulated
ENSG00000244509.4	APOBEC3C	19.1	130.51	-1.33	0.49	6.87E-03	2.41E-02	Downregulated
ENSG00000246273.9	SBF2-AS1	45.7	297.54	1.14	0.3	1.37E-04	7.77E-04	Upregulated
ENSG00000248079.4	DPH6-DT	13.58	59.26	-1.48	0.63	1.82E-02	5.48E-02	Downregulated
ENSG00000249738.10	ENSG00000249738	18.29	125.48	1.27	0.48	7.85E-03	2.70E-02	Upregulated
ENSG00000249846.7	LINC02021	9.83	86.8	-1.35	0.63	3.23E-02	8.79E-02	Downregulated
ENSG00000249856.1	ENSG00000249856	6.03	89.44	-2.24	0.88	1.14E-02	3.72E-02	Downregulated
ENSG00000251165.6	F11-AS1	12.29	69.22	-1.36	0.61	2.66E-02	7.51E-02	Downregulated
ENSG00000253626.4	EIF5AL1	724.43	2962.9	1.07	0.09	1.23E-31	7.15E-30	Upregulated
ENSG00000253669.4	GASAL1	15.69	54.64	1.48	0.58	1.11E-02	3.63E-02	Upregulated
ENSG00000254772.10	EEF1G	1870.28	24608.23	-1.39	0.06	4.43E-128	1.42E-125	Downregulated
ENSG00000254929.6	ENSG00000254929	11.11	251.5	1.14	0.54	3.41E-02	9.19E-02	Upregulated
ENSG00000257407.1	ENSG00000257407	36.69	37.55	-1.41	0.54	9.48E-03	3.18E-02	Downregulated
ENSG00000257443.2	LRIG3-DT	8.51	13.53	-2.13	1.01	3.52E-02	9.44E-02	Downregulated
ENSG00000257595.3	LINC02356	86.96	49.81	-1.5	0.4	1.96E-04	1.08E-03	Downregulated
ENSG00000259240.1	MIR4713HG	17.03	227.56	1.2	0.46	8.62E-03	2.93E-02	Upregulated
ENSG00000259803.8	SLC22A31	26.99	78.38	-1.13	0.47	1.69E-02	5.14E-02	Downregulated
ENSG00000259843.2	HEATR3-AS1	122.86	17.17	-2.04	0.48	2.25E-05	1.49E-04	Downregulated
ENSG00000260167.1	ENSG00000260167	13.87	71.16	-1.23	0.59	3.72E-02	9.88E-02	Downregulated
ENSG00000260983.2	ENSG00000260983	73.14	1066.63	-1.26	0.22	9.77E-09	1.13E-07	Downregulated
ENSG00000268089.3	GABRQ	16.13	51.42	1.42	0.59	1.62E-02	4.98E-02	Upregulated
ENSG00000270379.6	HEATR9	41.59	94.43	-1.24	0.42	3.32E-03	1.31E-02	Downregulated
ENSG00000277757.4	ENSG00000277757	15.73	148.97	-1.12	0.48	2.07E-02	6.09E-02	Downregulated
ENSG00000280560.3	LINC01374	259.2	910.21	-1.31	0.15	1.12E-17	3.08E-16	Downregulated
ENSG00000283777.2	CANX	15.73	1214.84	-1.05	0.4	8.88E-03	3.01E-02	Downregulated
ENSG00000285372.1	TNKS	11.21	79.04	-1.42	0.64	2.63E-02	7.44E-02	Downregulated
ENSG00000286046.1	ENSG00000286046	8.01	58.6	-2.07	0.77	6.96E-03	2.44E-02	Downregulated
ENSG00000286377.1	ENSG00000286377	54.46	10.05	-2.11	0.66	1.50E-03	6.55E-03	Downregulated
ENSG00000287526.1	ENSG00000287526	59.86	14.44	-1.57	0.63	1.23E-02	3.97E-02	Downregulated
ENSG00000288920.1	RPSAP58	123.66	5253.49	-1.23	0.16	2.24E-15	5.21E-14	Downregulated

RO Gene Enrichment

The GO term and KEGG pathway enrichment analyses show which functional gene categories and pathways are enriched in up- and downregulated genes from the volcano plot above. GO and KEGG analyses were performed with clusterProfiler's enrichGO and enrichKEGG functions. Within each domain are boxes for each gene ontology or KEGG term, and within each term are the contributing genes. The color of the gene box is the log₂ fold change between the two sample conditions while the size of the gene box is based off the -log₁₀(adjusted p-value) for the comparison. The color and size of the term boxes are based off the sum of all contributing genes. You can click on individual GO categories and subcategories to zoom and view their results in more detail. Clicking on the "Analysis" heading will restore the plot to its original appearance. For each gene box, the hover will show the adjusted p-value for the performed comparison and log₂ fold change of the listed gene. For each term, the hover will show the adjusted p-value for the enrichment analysis and the average fold change of all genes included in the box. Significance and fold changes are not provided for the domains.

This tab summarizes analyses performed on per-transcript basis, including determining codon usage, the detection of open reading frames (ORFs), and the identification of stalls.

ORF Detection

Open reading frames (ORFs) are regions of transcripts that undergo active translation. This barplot shows high confidence ORFs that were identified with ribotricer. For this plot, we required that the read density per ORF was ≥ 10, the read count was ≥ 50, and the ratio of codons with reads to total codons was ≥ 0.75. There are four main categories of reported ORFs:

Known: the ORF matches the annotated CDS
Downstream: the ORF is downstream of the annotated CDS and does not overlap the CDS
Upstream: the ORF is upstream of the annotated CDS and does not overlap the CDS
Novel: the ORF is located on a lncRNA.

Codon Usage

This scatter plot shows the average codon usage in each condition, where codon usage is defined as the scaled normalized frequency that P-sites were found to be enriched in each codon. Each dot is a different codon, colored by if it is a start, stop, or an amino acid-coding codon. Off-diagonal codons can indicate differential codon usage between the two conditions. Codon usage was determined using riboWaltz. If a gene has multiple transcripts, only the longest transcript is included in this analysis.

Stall Identification

RPF reads will accumulate where a ribosome pauses or stalls during translation. This plot shows putative stall locations for each transcript in the transcriptome, where stalls were detected per Shalgi et al. through the use of a Kolmogorov-Smirnov (KS) test on normalized cumulative P-site densities. Please note, this analysis is performed per transcript so listed distances refer to the distance in transcriptomic space not genomic space. The stall summary in the hover indicates the magnitude of the stall preceding the listed position relative to the coverage after the identified site.

This following files are provided along with this analysis:

File extension	Description	Help
.fastq.gz	Gzipped raw sequencing reads in FASTQ format.	A FASTQ file is a special type of text file that contains the sequencing data. Each read has four lines: Line 1: sequence identifier Line 2: the reported base calls Line 3: a separator Line 4: the quality scores
.bam .bai	BAM file containing unique sequence alignments to the genome. Reads aligned to repetitive elements were filtered out and PCR duplicates were removed. Multimapping reads are not included. Alignment indexes are also provided, and are required for visualization in a genome viewer.	A BAM file is a compressed binary file that contains a header (summarizing the entire file) and the aligned reads (read name, position, and alignment quality).
.pos.bw .neg.bw	Normalized bigwig file aligned to the positive (pos) and negative (neg) strand.	A bigWig track is a binary file that is used to visualize genome alignments. You can view these tracks in a genome browser such as IGV. We provide the data separated by the associated strand.
deseq_results.tsv	Results and statistics table for differential gene counts analysis using DESeq2 for the RPF and RNA-Seq libraries, and for the calculated ribosome occupancy.	Differentials were identified per gene, and following columns are provided in the DESeq2 outputs: gene_id: Ensembl's unique identifier and version of a gene gene_name: gene symbol for the examined gene baseMean: average DESeq2-normalized counts across all samples and all conditions. For RO analyses, the baseMean for the RNA-Seq and RPF libraries is provided. log2FoldChange: log₂-transformed ratio of expression between the two conditions lfcSE: log₂-transformed standard error stat: Wald's statistic pvalue: unadjusted measure of significance padj: false discovery rate (FDR) adjusted significance norm read count: DESeq2-normalized read counts for each sample. This is not provided for RO differentials. significance: written evaluation of the significance of the treatment effect on the gene.
translating_ORFs.tsv	Identified ORFs for each sample.	Each sample was analyzed with ribotricer and the unprocessed output file is provided. The following columns are included: ORF_ID: unique identifier for the ORF ORF_type: ribotricer's classification of the ORF. See ribotricer's documentation for more details status: indicates if the ORF is classified as translating based off its phase read_count: number of reads in the ORF length: length of the ORF valid_codons: number of codons with non-zero reads valid_codons_ratio: Ratio of codons with non-zero reads to the total number of codons read_density: total reads over the length of the ORF transcript_id: transcript identifier for the transcript associated with the ORF gene_id: gene identifier for the gene associated with the ORF gene_name: gene symbol for the gene associated with the ORF gene_type: classification of the gene associated with the ORF chrom: chromosome where the ORF is located strand: DNA strand for the ORF start_codon: codon sequence at the beginning of the ORF profile: reads per base across the length of the ORF
codon_usage.tsv	Table containing normalized codon frequency and codon usage for each sample.	Codon usage was determined using riboWaltz. If a gene has multiple transcripts, only the longest transcript is included in this analysis. The following columns are provided: codon: sequence of bases for the given codon _normalized_frequency: for each sample, the normalized frequency of in-frame P-sites in that codon. Normalization was done to the frequency of that codon appearing across all examined CDS sequences. _codon_usage: for each sample, the codon usage index for each codon. The codon usage index is a value between 0 and 1, a value closer to 1 indicates that codon was used more.
differential_stall.tsv	Table containing identified stalls within the Treated condition.	Counts for each codon in each transcript were obtained with riboWaltz. A Kolmogorov-Smirnov test was performed to identify transcripts with putative stalls. The following columns are included: transcript_id: unique transcript identifier gene_id: unique gene identifier for the linked transcript gene_name: gene symbol for the linked transcript stall_distance_from_annotated_start: distance of the stall from the annotated transcript start. Please note, the distance is in transcriptome space, not genomic space (in other words introns are removed) ks_d: Kolmogorov-Smirnov statistic (also called Kolmogorov's D statistic) pvalue: unadjusted significance of the stall padj: adjusted significance of the stall stall_summary: summary statistic for the degree of the stall. The magnitude indicates the degree of ribosome accumulation before the listed position reference: condition where the stall was identified
differential_loading.tsv	Table containing transcripts with changes in 5' loading.	Counts for each codon in each transcript were obtained with riboWaltz. Per Shalgi et al. counts were obtained in the first 16-195 bases of the CDS to the rest of the CDS. Counts were TPM normalized and the ratio between the beginning of the ORF and the end of the ORF was calculated. A pseudocount of 1 is added to both values to avoid divide by zero errors. transcript_id: unique transcript identifier gene_id: unique gene identifier for the linked transcript gene_name: gene symbol for the linked transcript len_five: length of the 5' end of the CDS in bases len_cds: length of the remaining part of the CDS in bases _five: per sample, the observed number of counts in bases 16-195 _cds: per sample, the observed number of counts in the remainder of the CDS _ratio: ratio of TPM normalized counts from the 5' end of the CDS to the TPM normalized counts from the rest of the CDS.
differential_readthrough.tsv	Table containing transcripts with changes in 3' readthrough.	Counts for each codon in each transcript were obtained with riboWaltz. Per Dunn et al. counts from the CDS were obtained for +12 bases after the start codon and -15 bases from the stop codon, and 3' UTR counts were obtained for +9 bases after the stop codon. The listed regions were excluded to avoid read contributions from the expected start and stop codon enrichment. Counts were TPM normalized and the ratio between the 3' UTR and the CDS was calculated. A pseudocount of 1 is added to both values to avoid divide by zero errors. transcript_id: unique transcript identifier gene_id: unique gene identifier for the linked transcript gene_name: gene symbol for the linked transcript len_utr3: length of the 3' UTR in bases len_cds: length of the CDS in bases _utr3: per sample, the observed number of counts in the 3' UTR _cds: per sample, the observed number of counts in the CDS _ratio: ratio of TPM normalized counts from the 3' UTR divided by the TPM normalized counts from the CDS
report.html	Report comparing libraries from RPF and RNA-Seq libraries for a given sample.	This interactive report summarizes information on a given sample for both the RNA-Seq and RPF libraries. The report can be viewed in an internet browser such as Google Chrome.
summary.report.html	Summary report comparing samples from two different conditions.	This interactive report summarizes information on the entire experiment. The report can be viewed in an internet browser such as Google Chrome.