Individual dataset pages provide for browsing or filtering, and facilitate integration of SPP with the research literature. To expose the SPP knowledgebase to biology researchers, we designed a web browser interface that accommodates a variety of routine data mining strategies depending upon the requirements of the end user. To provide for prediction of pathway node-target transcriptional regulatory relationships, we generated consensus ‘omics signatures, or consensomes, based on the significant differential expression or promoter occupancy of genomic targets across all underlying transcriptomic (expression array and RNA-Seq) or ChIP-Seq experiments. We then subjected over 10,000 publically archived transcriptomic or ChIP-Seq experiments to a biocuration pipeline that mapped them to their relevant signaling pathway node, BSM or biosample (tissue or cell line of study). Here, we designed a web knowledgebase, the Signaling Pathways Project (SPP), which incorporates stable community classifications of three major categories of cellular signaling pathway node (receptors, enzymes and transcription factors) and the bioactive small molecules (BSMs) known to modulate their functions. Unfortunately, a variety of obstacles prevent routine re-use of these datasets by bench biologists for hypothesis generation and data validation. Public transcriptomic and ChIP-Seq datasets have the potential to illuminate facets of transcriptional regulation by mammalian cellular signaling pathways not yet explored in the research literature.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |