Abstract:
:The ability to integrate 'omics' (i.e. transcriptomics and proteomics) is becoming increasingly important to the understanding of regulatory mechanisms. There are currently no tools available to identify differentially expressed genes (DEGs) across different 'omics' data types or multi-dimensional data including time courses. We present fCI (f-divergence Cut-out Index), a model capable of simultaneously identifying DEGs from continuous and discrete transcriptomic, proteomic and integrated proteogenomic data. We show that fCI can be used across multiple diverse sets of data and can unambiguously find genes that show functional modulation, developmental changes or misregulation. Applying fCI to several proteogenomics datasets, we identified a number of important genes that showed distinctive regulation patterns. The package fCI is available at R Bioconductor and http://software.steenlab.org/fCI/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Tang S,Hemberg M,Cansizoglu E,Belin S,Kosik K,Kreiman G,Steen H,Steen Jdoi
10.1093/nar/gkw157subject
Has Abstractpub_date
2016-06-02 00:00:00pages
e97issue
10eissn
0305-1048issn
1362-4962pii
gkw157journal_volume
44pub_type
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