FAQs - Frequently asked questions
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1. What is bioCompendium?

bioCompendium is a publicly accessible, high-throughput experimental data analysis platform. It helps in prioritizing the targets from gene expression analysis studies, from RNAi studies or from similar experiments. User can enter one or more gene lists with wide variety of accession/IDs or documents (pdf, doc, excel, ppt, html, ascii txt). bioCompendium compare, analyze and enrich the given gene list(s) against back-ground and show the results of comparison in colored bar diagrams. bioCompendium provides knowledge from biological databases, cluster the proteins based on sequence similarity or domain composition, does the pathway or GeneOnthology enrichments, provides the information about interacting drugs, metabolites, ligands, other chemicals and proteins. It also provides the transcription factor binding site (TFBS) profiles, diseases associations, orthology information, patent information (any of the protein or part of the protein form the given gene list(s) is already patented), clinical trails information and one can visualize the relationships in 2D and 3D visualization & download the gene list(s). bioCompendium can also be used to convert IDs from one format to other and to extract bio-entities from documents as of its secondary functionality.
2. How do we use bioCompendium?

bioCompendium take a list of accessions/IDs (one per line). It supports wide variety of ID types, please refer the 'ID/Document Type' dropdown menu for available ID types on 'home' page, each organism has few generic ID types and few organism specific ones. bioCompendium also takes documents (pdf, doc, excel, ppt, html, ascii txt) as input, in this case it will extract bio-entities from the documents using Reflect-API. Select the 'Primary organism' i.e organism of your interest (all the IDs in the given gene list(s)/documents converted to this organism based on orthology relations), then select 'Background',then select organism, give a name to gene list, upload gene list and/or document and select the corresponding 'ID/Document Type'
3. How many organisms bioCompendium currently covers?

bioCompendium currently covers 3 organisms - human, mouse and yest. We plan to extend to other model organisms in next releases.
4. What is primary organism?

User can select one of the 3 organisms (human, mouse or yeast) as a primary organism and it is the organism of user's interest, then all the gene list(s) will be mapped to the selected primary organism via the orthologous relationships.