Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC2115(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
|Motif Id||e-value||Consensus||Motif Logo|
Functional Enrichment for CAC2115
Module neighborhood information for CAC2115
|Gene||Common Name||Description||Module membership|
|CAC0437||CAC0437||Sensory transduction histidine kinase (NCBI ptt file)||53, 352|
|CAC0651||CAC0651||Hypothetical protein (NCBI ptt file)||292, 352|
|CAC0888||CAC0888||Phosphoglycerol transferase MdoB related protein, alkaline phosphatase superfamily (NCBI ptt file)||194, 352|
|CAC0949||CAC0949||Predicted transcriptional regulator (NCBI ptt file)||29, 352|
|CAC0993||dacF||D-alanyl-D-alanine carboxypeptidase (penicilin binding protein) (NCBI ptt file)||201, 352|
|CAC1285||CAC1285||Uncharacterized conserved protein, ortholog of YQEU B.subtilis (NCBI ptt file)||201, 352|
|CAC1286||CAC1286||Fe-S oxidoreductases (NCBI ptt file)||29, 352|
|CAC1292||CAC1292||Membrane protein containing HD superfamily hydrolase domain, YQFF ortholog (NCBI ptt file)||51, 283|
|CAC1293||CAC1293||Uncharacterized conserved predicted metal-binding protein, YQFG ortholog (NCBI ptt file)||51, 229|
|CAC1294||dgkA/pgpB||Diacylglycerol kinase (dgkA) fused to phosphatase B domain (pgpB) (NCBI ptt file)||51, 229|
|CAC1305||CAC1305||Uncharacterized protein similar to a protein from Cylindrotheca fusiformis plasmid (GI:99322) (NCBI ptt file)||51, 315|
|CAC1306||CAC1306||Hypothetical protein (NCBI ptt file)||5, 51|
|CAC1307||CAC1307||Hypothetical protein (NCBI ptt file)||51, 297|
|CAC1308||CAC1308||Uncharacterized low-complexity protein, related to YISX/YYBG B.subtilis (NCBI ptt file)||51, 317|
|CAC1309||CAC1309||Hypothetical protein (NCBI ptt file)||3, 51|
|CAC1489||CAC1489||Protein of phosphatidic acid phosphatase family, YNBD E.coli ortholog (NCBI ptt file)||286, 352|
|CAC1625||CAC1625||Phosphoserine phosphatase family protein (NCBI ptt file)||29, 51|
|CAC1710||CAC1710||Fe-S oxidoreductase, related to NifB/MoaA family with PDZ N-terminal domain (NCBI ptt file)||350, 352|
|CAC1736||recG||RecG helicase (NCBI ptt file)||3, 51|
|CAC1792||cdsA||CDP-diglyceride synthetase (NCBI ptt file)||282, 352|
|CAC1794||CAC1794||Predicted permease (NCBI ptt file)||3, 51|
|CAC1807||rpsO||Ribosomal Protein S15 (NCBI ptt file)||201, 352|
|CAC1818||CAC1818||Conserved membrane protein, possible 4-hydroxybenzoate octaprenyltranferase (NCBI ptt file)||3, 51|
|CAC1823||CAC1823||Uncharacterized conserved protein (NCBI ptt file)||51, 315|
|CAC1824||clpA||ATP-dependent Clp proteinase (NCBI ptt file)||51, 315|
|CAC1982||CAC1982||Predicted membrane protein (NCBI ptt file)||51, 317|
|CAC2065||deoB||Phosphopentomutase (NCBI ptt file)||51, 91|
|CAC2066||CAC2066||Integrase/recombinase XerD family (NCBI ptt file)||51, 91|
|CAC2067||CAC2067||Hypothetical protein (NCBI ptt file)||51, 268|
|CAC2068||CAC2068||Sporulation factor spoIIM, uncharacterized membrane protein (NCBI ptt file)||51, 268|
|CAC2115||lspA||Lipoprotein signal peptidase (NCBI ptt file)||51, 352|
|CAC2138||CAC2138||Exopolyphosphatase (NCBI ptt file)||2, 51|
|CAC2234||nifS||NifS family enzyme (cysteine desulfurase/cysteine sulfinate desulfinase) (NCBI ptt file)||51, 329|
|CAC2269||aspS||Aspartyl-tRNA synthetase (NCBI ptt file)||51, 329|
|CAC2270||CAC2270||Hypothetical protein (NCBI ptt file)||38, 352|
|CAC2285||ruvA||Holliday junction specific DNA helicase, subunit ruvA (NCBI ptt file)||25, 352|
|CAC2286||CAC2286||Uncharacterized protein, similar to protein from Clostridium histolyticum (GI:3892648) (NCBI ptt file)||292, 352|
|CAC2340||mutS1||DNA mismatch repair protein mutS, YSHD B.subtilis ortholog (NCBI ptt file)||51, 91|
|CAC2341||CAC2341||Collagenase family protease (NCBI ptt file)||51, 351|
|CAC2642||CAC2642||Predicted endonuclease (NCBI ptt file)||159, 352|
|CAC2672||CAC2672||Predicted membrane protein (NCBI ptt file)||5, 352|
|CAC2724||CAC2724||Hypothetical protein (NCBI ptt file)||51, 278|
|CAC2725||CAC2725||Predicted hydrolase from alpha/beta family, YQKD B.subtilis ortholog (NCBI ptt file)||51, 225|
|CAC2770||CAC2770||Amino acid transporter (NCBI ptt file)||3, 51|
|CAC3390||CAC3390||Response regulator (CheY-like receiver domain containing) (NCBI ptt file)||51, 297|
|CAC3391||CAC3391||Membrane associated signal transduction histidine kinase (NCBI ptt file)||51, 351|
Gene Page Help
If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.
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Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.
If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.
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Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.
Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.
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Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.
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CircVisOur circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
- 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
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