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July 30, 2022: iDEP updated to v0.96. Fixed a bug in the DEG1 tab regarding the different comparisons. iDEP now works even when factors have more than two levels. The downside is that some comparisons for non-reference levels are difficult to make. Users have to change the reference levels and rerun.

April 25, 2022: Gene ID conversion is much faster now, even when species has to be guessed. So is the DEG2 tab.

April 24, 2022: Add a tab for visualizing the fold-change of all genes in all KEGG diagrams across all comparisons!

Feb. 11, 2022: Like iDEP but your genome is not covered? Customized iDEP is now available. Its database includes several custom genomes requested by users. To request to add new species/genome, fill in this Form.

Email Jenny for questions. Dr. Ge is notorisly slow in responding to emails.

If it is slow, restart from a new browser window (not a new tab). You will be assigned to a new worker computer.

iDEP has not been thoroughly tested. Please let us know if you find any issue/bug.

iDEP: Integrated Differential Expression and Pathway analysis



Aspect ratios of figures can be adjusted by changing the width of browser window.

Enriched pathways for each cluster








Numbers of differentially expressed genes for all comparisons. "B-A" means B vs. A. Interaction terms start with "I:". Unnamed factors are at reference level.

In the demo data, if you select, "mu" and "mock" as reference levels for the two factors and select the interaction term, then "IR-mock" represents genes induced by IR in mutant, which lacks a functional P53 protein. "wt-mu" indicates genes differentially expressed in wt compared with mutant, under mock condition. The interaction term "I:p53_wt-Treatment_IR" tells us the extra response to IR in wildtype compared with mutant. In otherwords, this is the p53-dependent changes in gene expression in response to IR.

If you want to obtain the genes up- or down-regulated by IR in the wildtype, you will need to set the reference level for genotype to "wt" and rerun DESeq2. Similarily, to obtain the DEGs between mutant and wildtype, both with IR, set the reference level for treatment as IR and rerun DESeq2.


Enriched pathways in DEGs for the selected comparison:

Top Genes for selected comparison:

Red and blue indicates activated and suppressed pathways, respectively.
Red and blue indicates activated and suppressed pathways, respectively.
Red and green represent up- and down-regulated genes, respectively.
Bright red indicates most upregulated; bright green, most downregulated.

Enriched gene sets in selected bicluster



Genes in this cluster



Enriched pathways among all genes in selected module

Email us for questions, suggestions, or data contributions. Stay connected via user group or Twitter. Visit our GitHub page to see source code, install a local version, or report bugs and request features. iDEP is being developed by a very small team: Dr. Xijin Ge and a graduate student (Homepage).

R as in Reproducibility

Documentation site. Source code on GitHub, where users can also report bugs or requet features.
To improve reproducibility, iDEP generates custom R code based on your data and choices of parameters. Users with some R coding experience should be able to re-run most analyses by downloading all of the files below. If Ensembl IDs is not used in users' original file, we should use the converted data file. Click through all the tabs and then download all these file to a folder. Run the Customized R code or the Markdown file. R Markdown example.
Customized R code Customized R code(Markdown) iDEP core functions Gene Info file Pathway file (large)

All versions of iDEP

iDEP 0.96 with Ensembl Release 104, released July 30, 2022
iDEP 0.95 with Ensembl Release 104, released Feb. 8, 2022
iDEP 0.94 with Ensembl Release 104, released on Oct. 15, 2021
iDEP 0.93 with Ensembl Release 103, released May 20, 2021
iDEP 0.92 with Ensembl Release 100, released May 20, 2021
iDEP 0.90 with Ensembl Release 96, released May 19, 2021
iDEP 0.85 with Ensembl Release 95, released March 29, 2019
iDEP 0.82 with Ensembl Release 92, released July 11, 2018
iDEP 0.73 with Ensembl Release 91, released December 2017

Citation

Please cite: Ge SX, Son EW, Yao R: iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. BMC Bioinformatics 2018, 19(1):534. PMID:30567491 Full text

Usage Statistics

As of May 11 2021, iDEP website has been visited 167832 times by 43,220 users from 100+ countries. iDEP has been used by researchers to analyze transcriptomic data from sun flowers to primates to human, as demonstrated by the 191 papers citing iDEP.



Changes

v 0.38 Gene ID conversion, remove redudancy; rlog option set to blind=TRUE.
v 0.39 Reorganized code. Updated to Bioconductor 3.5; solved problems with PREDA 9/8/17.
v 0.40 Moved libraries from the beginning to different places to save loading time.
v 0.50 Enable changing colors for heatmap. Fixed error with voom; also changed method to TMM, see here.
2/5/2018 V 0.62 : Add tree and networks to visualize overlaps between enriched gene sets, in K-means, DEG2, and pathway tags. Downloads of pathway analysis results and high-resolution figures.
2/6/2018: Fixed errors caused by gene symbol matching for unknown species. More user control of hierarchical clustering tree
2/9/2018: V 0.65 Added API access to STRINGdb website on the DEG2 tab. Supports thousands of bacterial species
2/10/2018: V 0.66 Improved API access to STRINGdb, by adding automatic species matching.
2/11/2018: V 0.67 Tested with larger dataset of 259 samples. Changed figure configurations.
2/14/2018: V 0.68 Fixed Pathview loading code. Connected Pathview to PGSEA.
2/25/2018: V 0.68 Fixed Fold-change, FDR data upload and parsing. Figure resolution using the res=150 option help improve readability of labels.
2/28/2018: V0.69 Change interactive heat maps to re-order columns
3/12/2018: V0.70 Generating R code and downloading annotation files used in analysis.
3/14/2018: V0.71 Improve R markdown file; add color to EDA plots; detect bias in sequencing depth
3/18/2018: v0.711 Fixed error caused by gene names containing characters such as ' or "
3/28/2018: v0.712 Fine tuned EDA plots
4/3/2018: V0.713 add permutations for fgsea. Expand quotes.
4/13/2018: V0.72 fixed bug caused error in R Markdown file when users choose species other than the default.
4/25/2018: V0.73 Fixed bug for GO terms tree in k-Means. Added layout button for network viz of GO terms
5/28/2018: V0.73 Enabled download of all FDR and fold-changes at the DEG1 tab. Problem with the FDR and fold-change data with only one columns.
7/28/2018: v0.80 New v0.80 Updated annotation database. Comprehensive pathway database for human. TF binding motifs for 200+ speceis. Old version made available.
7/29/2018: v0.80 Orgized UI.R according to Google R style guide.
7/30/2018: V0.80 Fixed error in downloaded up- and down-regulated gene lists. We thank Juan Xie for pointing this out.
12/2/2018: v0.81 High resolution figure download with eps format, which can be eidted with Adobe Illustrator.
3/5/2019: v0.82 Fix a bug regarding limma for identification of D.E.Gs. Up- and down-regulation are opposite in some cases.
3/29/2019: v0.85 Annotation database upgrade. Ensembl v 95. Ensembl plants v.42, and Ensembl Metazoa v.42.
5/19/2019: v0.90 Annotation database upgrade. Ensembl v 96. Ensembl plants v.43, and Ensembl Metazoa v.43. STRING-db v10
2/3/2020: v0.90 customizable PCA plot and scatter plot
5/10/2021: V0.93 updated to Ensembl Release 103 and String-DB v11.
10/15/21: For GO enrichment analysis, we now recommend using background genes, instead of all genes on the genome. In the KNN and DEG2 tabs, it is now the default that all genes passed the filter in Pre-Process tab are used as a customized background.

10/18/20: Interactive network enabling users to easily visualize the relatedness of significant pathways similar to EnrichmentMap.

April 23, 2022: KEGG diagram on the Pathway tab is now working! Please email Jenny if you see any issues!

April 23, 2022: DEG2 tab is now much faster! I hope people complained about it earlier!

April 20, 2022: Plot one or more genes is now working. Bug fixed.

Mar. 7, 2022: Fixed an R library issue affected KEGG diagrams for some organisms.

Feb. 19, 2022: R upgraded from 4.05 to 4.1.2. This solved the STRING API issues. Some Bioconductor packages are also upgraded.

Feb. 8, 2022: iDDEP v0.95 becomes default. Old versions are still available. See the last tab.

Nov. 15, 2021: iDEP v0.95 available in testing mode. It includes Ensembl database update, new species from Ensembl Fungi and Ensembl Protists, and STRINGdb (5090 species) update from v11 to 11.5.

10/26/2021: The Genome view is now much improved! Automatically detects chromosomal regions enriched with genes having abnormaly high and low fold-changes.

10/15/21: For GO enrichment analysis, we now recommend using background genes, instead of all genes on the genome. In the KNN and DEG2 tabs, it is now the default that all genes passed the filter in Pre-Process tab are used as a customized background.

We updated instruction for local installation here. The most recent database file is now publically available, free of charge for non-profit organizations.

Check out the 50,000+ datasets of uniformly processed public RNA-seq data here!

10/18/20: Interactive network enables users to easily visualize the relatedness of pathways, similar to EnrichmentMap. Using the Network buttons on DEG2 and Pathway tabs, you can generate and export interactive networks like this one below. You can move the nodes by dragging them, zoom in by scrolling, and shift the entire network by click on an empty point and drag.



In loving memory of my parents. X.G.