dorsal/arxiv
View SchemaElucidation of Directionality for Co-Expressed Genes: Predicting Intra-Operon Termination Sites
| Authors | Anshuman Gupta, Costas D. Maranas, Reka Albert |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0511029 |
| URL | https://arxiv.org/abs/q-bio/0511029 |
| DOI | 10.1093/bioinformatics/bti780 |
| Journal | Bioinformatics 22(2):209-214 (2006) |
Abstract
We present a novel framework for inferring regulatory and sequence-level information from gene co-expression networks. The key idea of our methodology is the systematic integration of network inference and network topological analysis approaches for uncovering biological insights. We determine the gene co-expression network of Bacillus subtilis using Affymetrix GeneChip time series data and show how the inferred network topology can be linked to sequence-level information hard-wired in the organism's genome. We propose a systematic way for determining the correlation threshold at which two genes are assessed to be co-expressed by using the clustering coefficient and we expand the scope of the gene co-expression network by proposing the slope ratio metric as a means for incorporating directionality on the edges. We show through specific examples for B. subtilis that by incorporating expression level information in addition to the temporal expression patterns, we can uncover sequence-level biological insights. In particular, we are able to identify a number of cases where (i) the co-expressed genes are part of a single transcriptional unit or operon and (ii) the inferred directionality arises due to the presence of intra-operon transcription termination sites.
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"abstract": "We present a novel framework for inferring regulatory and sequence-level\ninformation from gene co-expression networks. The key idea of our methodology\nis the systematic integration of network inference and network topological\nanalysis approaches for uncovering biological insights. We determine the gene\nco-expression network of Bacillus subtilis using Affymetrix GeneChip time\nseries data and show how the inferred network topology can be linked to\nsequence-level information hard-wired in the organism\u0027s genome. We propose a\nsystematic way for determining the correlation threshold at which two genes are\nassessed to be co-expressed by using the clustering coefficient and we expand\nthe scope of the gene co-expression network by proposing the slope ratio metric\nas a means for incorporating directionality on the edges. We show through\nspecific examples for B. subtilis that by incorporating expression level\ninformation in addition to the temporal expression patterns, we can uncover\nsequence-level biological insights. In particular, we are able to identify a\nnumber of cases where (i) the co-expressed genes are part of a single\ntranscriptional unit or operon and (ii) the inferred directionality arises due\nto the presence of intra-operon transcription termination sites.",
"arxiv_id": "q-bio/0511029",
"authors": [
"Anshuman Gupta",
"Costas D. Maranas",
"Reka Albert"
],
"categories": [
"q-bio.MN",
"q-bio.GN"
],
"doi": "10.1093/bioinformatics/bti780",
"journal_ref": "Bioinformatics 22(2):209-214 (2006)",
"title": "Elucidation of Directionality for Co-Expressed Genes: Predicting Intra-Operon Termination Sites",
"url": "https://arxiv.org/abs/q-bio/0511029"
},
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