Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC2201(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|
Module neighborhood information for CAC2201
|Gene||Common Name||Description||Module membership|
|CAC0274||ansB||Aspartate ammonia-lyase (aspartase) gene ansB(aspA) (NCBI ptt file)||206, 238|
|CAC0279||CAC0279||Peptidil-prolyl cis-trans isomerase (NCBI ptt file)||251, 348|
|CAC0324||CAC0324||TPR repeats containing protein (NCBI ptt file)||25, 348|
|CAC0556||CAC0556||Uncharacterised conserved protein (NCBI ptt file)||34, 238|
|CAC0641||CAC0641||Uncharacterized conserved protein (NCBI ptt file)||109, 348|
|CAC0650||CAC0650||Adenilate cyclase, class2 (thermophilic) (NCBI ptt file)||20, 348|
|CAC0690||CAC0690||Endoglucanase, aminopeptidase M42 family (NCBI ptt file)||216, 238|
|CAC0693||CAC0693||Transcriptional regulator of the LacI family (NCBI ptt file)||176, 238|
|CAC0751||CAC0751||Permease (NCBI ptt file)||322, 348|
|CAC0876||CAC0876||Transcriptional regulator, MarR/EmrR family (NCBI ptt file)||77, 348|
|CAC0877||cfa||Cyclopropane fatty acid synthase (NCBI ptt file)||77, 348|
|CAC0957||CAC0957||Xre family DNA-binding domain and TPR-repeat-containing protein (NCBI ptt file)||298, 348|
|CAC0958||CAC0958||Xre family DNA-binding domain and TPR-repeat-containing protein (NCBI ptt file)||348, 365|
|CAC1001||CAC1001||Aspartate aminotransferase (NCBI ptt file)||34, 348|
|CAC1002||CAC1002||Nicotinic acid phosphoribosyltransferase (NCBI ptt file)||49, 348|
|CAC1036||pykA||Pyruvate kinase (NCBI ptt file)||348, 359|
|CAC1047||CAC1047||Ribonucleotide reductase, vitamin B12-dependent (NCBI ptt file)||231, 238|
|CAC1096||CAC1096||Uncharacterized protein, YjiN homolog (NCBI ptt file)||277, 348|
|CAC1172||CAC1172||Predicted integrase of XerC/XerD family, diverged (NCBI ptt file)||151, 238|
|CAC1238||CAC1238||Hypothetical protein (NCBI ptt file)||62, 348|
|CAC1262||CAC1262||Predicted nucleotidyltransferases of NarD/TagD family (N-term. domain) , yqeJ ortholog (NCBI ptt file)||31, 238|
|CAC1436||CAC1436||Hypothetical protein (NCBI ptt file)||261, 348|
|CAC1626||CAC1626||Glycerol dehydrogenase (NCBI ptt file)||222, 238|
|CAC1666||CAC1666||Predicted membrane protein (NCBI ptt file)||113, 238|
|CAC1669||CstA||Carbon starvation protein (NCBI ptt file)||209, 238|
|CAC1856||CAC1856||Ribonuclease HI (NCBI ptt file)||238, 267|
|CAC1868||CAC1868||Uncharacterized secreted protein, homolog YXKC Bacillus subtilis (NCBI ptt file)||152, 348|
|CAC1943||CAC1943||Hypothetical protein (NCBI ptt file)||238, 348|
|CAC2019||CAC2019||Malonyl CoA-acyl carrier protein transacylase (NCBI ptt file)||166, 238|
|CAC2064||deoD||Purine nucleoside phosphorylase (NCBI ptt file)||182, 238|
|CAC2182||CAC2182||Hypothetical protein (NCBI ptt file)||209, 348|
|CAC2197||CAC2197||Aminoglycoside N3'-acetyltransferase (NCBI ptt file)||157, 348|
|CAC2200||CAC2200||Uncharacterized conserved protein (NCBI ptt file)||238, 299|
|CAC2201||CAC2201||Hypothetical protein (NCBI ptt file)||238, 348|
|CAC2377||oppA||Oligopeptide ABC-type transporter, periplasmic binding component (Frameshift) (NCBI ptt file)||299, 348|
|CAC2549||CAC2549||Uncharacterized conserved protein (NCBI ptt file)||92, 348|
|CAC2688||CAC2688||Alpha/beta superfamily hydrolase (possible chloroperoxidase) (NCBI ptt file)||67, 238|
|CAC2979||aspS||Aspartyl-tRNA synthetase (NCBI ptt file)||37, 238|
|CAC3062||CAC3062||CPSB/CAPC ortholog, PHP family hydrolase (NCBI ptt file)||238, 251|
|CAC3063||CAC3063||Transcriptional regulator, LytR family (NCBI ptt file)||238, 365|
|CAC3295||CAC3295||Probable cation efflux pump (multidrug resistance protein) (NCBI ptt file)||77, 348|
|CAC3589||CAC3589||Uncharacterized conserved membrane protein, YHGE B.subtilis ortholog (NCBI ptt file)||238, 303|
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.
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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;
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