Elucidating functional context within microarray data by integrated transcription factor-focused gene-interaction and regulatory network analysis.
Microarrays do not yield direct evidence for functional connections between genes. However, transcription factors (TFs) and their binding sites (TFBSs) in promoters are important for inducing and coordinating changes in RNA levels, and thus represent the first layer of functional interaction. Similar to genes, TFs act only in context, which is why a TF/TFBS-based promoter analysis of genes needs to be done in the form of gene(TF)-gene networks, not individual TFs or TFBSs. In addition, integration of the literature and various databases (e.g. GO, MeSH, etc) allows the adding of genes relevant for the functional context of the data even if they were initially missed by the microarray as their RNA levels did not change significantly. Here, we outline a TF-TFBSs network-based strategy to assess the involvement of transcription factors in agonist signaling and demonstrate its utility in deciphering the response of human microvascular endothelial cells (HMEC-1) to leukemia inhibitory factor (LIF). Our strategy identified a central core of eight TFs, of which only STAT3 had previously been definitively linked to LIF in endothelial cells. We also found potential molecular mechanisms of gene regulation in HMEC-1 upon stimulation with LIF that allow for the prediction of changes of genes not used in the analysis. Our approach, which is readily applicable to a wide variety of expression microarray and next generation sequencing RNA-seq results, illustrates the power of a TF-gene networking approach for elucidation of the underlying biology.
['Werner|Thomas|T|', 'Dombrowski|Susan M|SM|', 'Zgheib|Carlos|C|', 'Zouein|Fouad A|FA|', 'Keen|Henry L|HL|', 'Kurdi|Mazen|M|', 'Booz|George W|GW|']
D001665:Binding Sites D002460:Cell Line D042783:Endothelial Cells D015870:Gene Expression D005786:Gene Expression Regulation D053263:Gene Regulatory Networks D059014:High-Throughput Nucleotide Sequencing D006801:Humans D053605:Leukemia Inhibitory Factor D020411:Oligonucleotide Array Sequence Analysis D011401:Promoter Regions, Genetic D012313:RNA D050796:STAT3 Transcription Factor D015398:Signal Transduction D014157:Transcription Factors
transcription factors high-throughput (HT) approaches microarray data analysis transcription factor binding sites transcription factor-gene networking