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Please use this identifier to cite or link to this item:
http://krishi.icar.gov.in/jspui/handle/123456789/42547
Full metadata record
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Hukam C Rawal | en_US |
dc.contributor.author | Ulavappa Angadi | en_US |
dc.contributor.author | Tapan Kumar Mondal | en_US |
dc.date.accessioned | 2020-11-23T06:51:08Z | - |
dc.date.available | 2020-11-23T06:51:08Z | - |
dc.date.issued | 2020-09-02 | - |
dc.identifier.citation | Not AvailableRawal HC, Angadi U, Mondal TK. TEnGExA: an R package based tool for tissue enrichment and gene expression analysis. Brief Bioinform. 2020 Sep 22:bbaa221. doi: 10.1093/bib/bbaa221. Epub ahead of print. PMID: 32960209. | en_US |
dc.identifier.issn | 44107488 | - |
dc.identifier.uri | http://krishi.icar.gov.in/jspui/handle/123456789/42547 | - |
dc.description | Not Available | en_US |
dc.description.abstract | RNA-seq data analysis with rapidly advancing high-throughput sequencing technology, nowadays provides large number of transcripts or genes to perform downstream analysis including functional annotation and pathway analysis. However for the data from multiple tissues, downstream analysis with tissue-specific or tissue-enriched transcripts is highly preferable. However, there is still a need of tool for quickly performing tissue-enrichment and gene expression analysis irrespective of number of input genes or tissues at various fragments per kilobase of transcript per million fragments mapped (FPKM) thresholds. To fulfill this need, we presented a freely available R package and web-interface tool, TEnGExA, which allows tissue-enrichment analysis (TEA) for any number of genes or transcripts for any species provided only a read-count or FPKM-value matrix as input. Based on the different FPKM value and fold thresholds, TEnGExA classifies the user provided gene lists into tissue-enriched or tissue-specific transcripts along with other standard classes. By analyzing the published sample data from human, plant and microorganism, we signifies that TEnGExA can easily handle complex or large data from any species to provided tissue-enriched gene list for downstream analysis in quick time. In summary, TEnGExA is quick, easy to use and an efficient tool for TEA. The R package is freely available at https://github.com/ubagithub/TEnGExA/ and the GUI web interface is accessible at http://webtom.cabgrid.res.in/tissue_enrich/. | en_US |
dc.description.sponsorship | Not Available | en_US |
dc.language.iso | English | en_US |
dc.publisher | Not Available | en_US |
dc.relation.ispartofseries | 10;1093 | - |
dc.subject | FPKM | en_US |
dc.subject | gene expression | en_US |
dc.subject | read-count | en_US |
dc.subject | tissue-enrichment | en_US |
dc.subject | tissue-specific | en_US |
dc.title | TEnGExA: an R package based tool for tissue enrichment and gene expression analysis | en_US |
dc.title.alternative | Not Available | en_US |
dc.type | Research Paper | en_US |
dc.publication.projectcode | Not Available | en_US |
dc.publication.journalname | Briefings in Bioinformatics | en_US |
dc.publication.volumeno | 10 | en_US |
dc.publication.pagenumber | 1093 | en_US |
dc.publication.divisionUnit | Centre for Agricultural Bioinformatics | en_US |
dc.publication.sourceUrl | 10.1093/bib/bbaa221 | en_US |
dc.publication.sourceUrl | https://doi.org/10.1093/bib/bbaa221 | en_US |
dc.publication.authorAffiliation | ICAR::National Institute for Plant Biotechnology | en_US |
dc.publication.authorAffiliation | ICAR::Indian Agricultural Statistics Research Institute | en_US |
dc.ICARdataUseLicence | http://krishi.icar.gov.in/PDF/ICAR_Data_Use_Licence.pdf | en_US |
dc.publication.naasrating | Not Available | - |
Appears in Collections: | AEdu-IASRI-Publication |
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