Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC3577(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 CAC3577
Module neighborhood information for CAC3577
|Gene||Common Name||Description||Module membership|
|CAC0224||CAC0224||Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file)||3, 91|
|CAC0229||CAC0229||Predicted Zn-dependent proteases, TLDD ortholog (NCBI ptt file)||91, 225|
|CAC0230||CAC0230||Inactivated predicted Zn-dependent protease, PMBA ortholog (NCBI ptt file)||91, 225|
|CAC0270||CAC0270||Hypothetical protein (NCBI ptt file)||67, 225|
|CAC0290||CAC0290||Sensory transduction histidine kinases (NCBI ptt file)||82, 91|
|CAC0400||CAC0400||Hypothetical protein, CF-19 family (NCBI ptt file)||91, 346|
|CAC0433||CAC0433||Methyl-accepting chemotaxis protein (NCBI ptt file)||20, 225|
|CAC0482||CAC0482||Zn-dependent hydrolases of the metallo-beta-lactamase superfamily (NCBI ptt file)||225, 239|
|CAC0602||ftsH||ATP-dependent zinc metallopeptidase FtsH (cell dividion protein) (NCBI ptt file)||91, 222|
|CAC0603||CAC0603||Superfamily I DNA and RNA helicase (NCBI ptt file)||91, 225|
|CAC0764||CAC0764||NADPH-dependent glutamate synthase beta chain (NCBI ptt file)||44, 91|
|CAC0825||CAC0825||Endoglucanase family 5 (NCBI ptt file)||225, 261|
|CAC1540||CAC1540||Uncharacterized ATP-grasp enzyme (NCBI ptt file)||71, 91|
|CAC1544||CAC1544||Cytidine deaminase, cdd (NCBI ptt file)||91, 225|
|CAC1546||deoA||Pyrimidine-nucleoside phosphorylase (NCBI ptt file)||91, 200|
|CAC1717||CAC1717||Uncharacterized conserved protein, YLOA ortholog (NCBI ptt file)||3, 91|
|CAC1796||CAC1796||Predicted membrane-associated Zn-dependent protease (NCBI ptt file)||64, 91|
|CAC1909||rnd||Ribonuclease D (NCBI ptt file)||225, 277|
|CAC1910||CAC1910||Predicted membrane protein (NCBI ptt file)||225, 277|
|CAC2065||deoB||Phosphopentomutase (NCBI ptt file)||51, 91|
|CAC2066||CAC2066||Integrase/recombinase XerD family (NCBI ptt file)||51, 91|
|CAC2139||flgG||Flagellar basal body rod protein (NCBI ptt file)||192, 225|
|CAC2296||CAC2296||Uncharacterized protein, YigZ family (NCBI ptt file)||3, 91|
|CAC2297||CAC2297||Transcriptional regulator of MocR family (DNA-binding HTH domain and aminotransferase domain) (NCBI ptt file)||3, 91|
|CAC2298||CAC2298||Predicted nucleotidyltransferase (NCBI ptt file)||91, 345|
|CAC2337||CAC2337||Phosphomannomutase (NCBI ptt file)||225, 294|
|CAC2340||mutS1||DNA mismatch repair protein mutS, YSHD B.subtilis ortholog (NCBI ptt file)||51, 91|
|CAC2415||CAC2415||Uncharacterized conserved protein (NCBI ptt file)||91, 289|
|CAC2450||CAC2450||Desulfoferrodoxin (NCBI ptt file)||80, 225|
|CAC2601||CAC2601||S-adenosylmethionine decarboxylase (NCBI ptt file)||82, 225|
|CAC2634||CAC2634||Ferric uptake regulator (FUR family), YGAG B.subtilis ortholog (NCBI ptt file)||49, 225|
|CAC2725||CAC2725||Predicted hydrolase from alpha/beta family, YQKD B.subtilis ortholog (NCBI ptt file)||51, 225|
|CAC2736||sbcC||ATPase involved in DNA repair (NCBI ptt file)||91, 98|
|CAC2785||CAC2785||Hypothetical protein (NCBI ptt file)||134, 225|
|CAC2897||CAC2897||Predicted UDP-glucuronosyltransferase, YPFP B/subtilis ortholog (NCBI ptt file)||225, 286|
|CAC2914||panB||Ketopantoate hydroxymethyltransferase (NCBI ptt file)||225, 235|
|CAC3085||CAC3085||TPR-repeat-containing protein; Cell-adhesion domain (NCBI ptt file)||225, 344|
|CAC3086||CAC3086||Protein containing cell adhesion domain (NCBI ptt file)||225, 344|
|CAC3248||CAC3248||Hypothetical protein (NCBI ptt file)||157, 225|
|CAC3249||CAC3249||Hypothetical protein (NCBI ptt file)||157, 225|
|CAC3251||CAC3251||Sensory transduction protein containing HD_GYP domain (NCBI ptt file)||63, 225|
|CAC3267||CAC3267||Specialized sigma subunit of RNA polymerase (NCBI ptt file)||99, 225|
|CAC3299||bdhA||NADH-dependent butanol dehydrogenase A (BDH I) (NCBI ptt file)||91, 100|
|CAC3392||CAC3392||NADH-dependent butanol dehydrogenase (NCBI ptt file)||62, 91|
|CAC3518||CAC3518||Transcriptional regulators, AcrR family (NCBI ptt file)||225, 359|
|CAC3570||accC||Biotin carboxylase (NCBI ptt file)||44, 225|
|CAC3571||fabZ||Hydroxymyristoyl-(acyl carrier protein) dehydratase (NCBI ptt file)||65, 91|
|CAC3572||accB||Biotin carboxyl carrier protein of acetyl-CoA carboxylase (NCBI ptt file)||44, 91|
|CAC3577||acp||Acyl Carrier Protein, ACP (NCBI ptt file)||91, 225|
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.
Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.
Module Members Tab
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.
- 2. Source gene
- 3. Target genes (other module members)
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- 5. Module(s) that source gene and target genes belong to
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