Send an email to help make sure iDEP continue to exist. We are writing a grant proposal (due June 5th) to NIH to seek support for the development and maintenance of iDEP. A brief email on how this tool helped your research would go a long way to support our tiny team, even if you are a graduate student.
Email
New v0.70 iDEP generates R and R Markdown codes for users to run in stand-alone!
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.
Using genes whose maximum expression level is at top 75%. Data is transformed and clustered as specified in the main page.
Heatmap with hierarchical clustering tree
Mouse over to see gene names. To zoom, click and drag up or downward and release.
Distribution of variations among genes
Enriched pathways for each cluster
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.
Distribution of variations among genes
Visualize enrichment
Gene sets closer on the tree share more genes. Sizes of dot correspond to adjuested Pvalues
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.
Enriched pathways among all genes in selected module
Choose soft threshold
Heatmap of identified modules
Email us
for questions, suggestions, or data contributions. Stay connected via
user group
or
Twitter
.
R as in Reproducibility
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.
iDEP v0.62 2/5/2018: 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.