New v0.68! Try the STRING-db API access on the DEG2 page that offer
protein interaction networks and GO enrichment for thousands species, including bacteria.
Enriched TF binding motifs in promoters of Kmeans clusters
Determining the number of clusters (k)
Following the elbow method, one should choose k so that adding another cluster
does not substantially reduce the within groups sum of squares.
Wikipedia
t-SNE plot of genes
We use the dimension reduction algorith
t-SNE
to map the top genes. Examine the distribution can help choose the nubmer of clusters in k-Means.
Enrichment and network visualization using STRING API
iDEP tries to match your species with the 115 archaeal,
1678 bacterial, and 238 eukaryotic species in the
STRING server
and send the DEGs. If it is running, please wait until it finishes. This can take 5 minutes
especially for the first time when iDEP downloads large annotation files.
Analyze top DEGs on protein interaction networks (PPIs)
By sending top DEGs (ranked by fold-change) to the STRING website,
iDEP is retrieving a sub-network, calculating PPI enrichment,
and generating custom URLs to the STRING website containing your genes.
This can take 5 minutes. Patience will pay off!
Interactions among proteins encoded by top up-regulated proteins
Enriched TF binding motifs in promoters of DEGs
Red and blue indicates activated and suppressed pathways, respectively.
Red and blue indicates activated and suppressed pathways, respectively.
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.
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 Feb. 8, 2019, iDEP website has been visited 16,344 times by 4,500 users from 80 countries.
Fully functional only in early 2018, iDEP has been used by researchers to analyze transcriptomic data
from sun flowers to primates to human,
as demonstrated by 12 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.
