# Requested feature No of user requests Status
1 Implement miRNA enrichment analysis 33 Completed
2 Venn diagram between Vesiclepedia and my dataset(s) 26 Completed
3 Generate heatmaps for input datasets 24 Completed
4 Improved coverage of UniProt IDs 24 Completed
5 Mac or linux compatitbility or web based FunRich version 21 In progress
6 Real time database update 20 Completed
7 Compare more than two input datasets for enrichment analysis 19 Completed
8 Option to customize the color of charts/graphs 18 Completed
9 Download proteins/RNA identified in extracellular vesicles isolated from a specific sample 16 Completed
10 Download proteins/RNA identified exclusively in a subtype of extracellular vesicle 16 Completed
11 Regular update of background databases 16 Completed
12 Download top 100 proteins identified in extracellular vesicles 14 Completed
13 Allow users to control the databases 14 Completed
14 Download all proteins/RNA identified in a subtype of extracellular vesicle 13 Completed
15 Enrichment of genes in different cancer types using COSMIC data 13 Completed
16 Save workspace or session feature 12 Completed
17 Option to upload miRNA gene name or miRbase acession number 12 Completed
18 Quantitative expression profile based enrichment analysis 11 Completed
19 Implement metabolomic enrichment analysis 10 In progress
20 Update Vesiclepedia data automatically 10 Completed
21 Mapping and conversion of acession IDs to different databases 10 Completed
22 Venn diagram of the Vesiclepedia would benefit from displaying distribution of the sample genes by EV subtypes 9 Completed
23 Description of the Vesiclepedia section in the manual 8 Completed
24 For each protein resulting shared using Venn diagram tool to specify type of experiment through which it was identified in exosomes and provide the link to PubMed references supporting its identification 8 Completed
25 Description or full name that can appear on mouse click or as a pop up window for terms/domains 7 Completed
26 Option to choose more databases to use as background for heatmaps 7 Completed
27 For each protein in the lists derived from Venn diagram report in which type of sample it was identified 7 Completed
28 Ability to download the top hits (protein/ mRNA/ miRNA/ lipids) 7 Completed
29 Ability to search for proteins that are being currently used. Especially important if you are looking for a protein / bunch of proteins amongst several hundreds in the list 7 Completed
30 Edit font of all charts/graphs 7 Completed
31 Refer the nature or source of the interaction in interaction maps (text mining or experimental) 6 In progress
32 Ability to find the references of filtered dataset when comparing custom dataset with the filtered dataset from Vesiclepedia 6 Completed
33 Identify upregulated and downregulated proteins for specific biological process from heatmap data 6 Completed
34 Suggestions for the manual: for a first-time user, a description of the input data (examples would suffice) would be necessary 6 Completed
35 Upload data from an Excel sheet 6 Completed
36 For each protein list from the Venn diagram, provide, if available, the link to its interactome 5 Completed
37 More cancer types under the cell lines tab 5 Completed
38 Content types should also include other molecules including lncRNAs, piRNA, snoRNA or can be listed as other RNA molecules. 5 In progress
39 Set a default output option which allows to export a summary report including excel files, image files and a summary text 5 Completed
40 Clustered heatmap 5 Completed
41 Under the tissue/cell types include CSF 4 Completed
42 Reflect the fragmentation status of the vesicular RNAs (fragmented vs. intact) 4 In progress
43 Implement quantitative Venn diagram of differentially expressed genes/proteins 3 Completed
44 Include videos for custom database upload 3 Completed
45 Implement Recatome pathway enrichment and automatic download of database 3 Completed
46 Implement Gene Ontology enrichment and automatic download of database 3 Completed
47 Display graphs/charts in Excel sheet automatically 3 Completed
48 Find targets for miRNA 3 Completed
49 Heatmap of interested genes (not clustered) 2 Completed
50 Enrichment analysis using quantitative values 2 Completed
51 Convert Gene Symbol to UniProt IDs 2 Completed
52 Find which miRNA will bind to my gene list 1 Completed
53 Implement q value method (Storey and Tibshirani) 1 Completed
54 Protein-protein interaction for other species (non human) 1 Completed