Organism : Clostridium acetobutylicum | Module List :
Phage related transcriptional regulator (Xre family) (NCBI ptt file)
Functional Annotations (1)
|sequence-specific DNA binding||go/ molecular_function|
Regulation information for CAC1947(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 CAC1947
|sequence-specific DNA binding||go/ molecular_function|
Module neighborhood information for CAC1947
|Gene||Common Name||Description||Module membership|
|CAC0004||recF||RecF, ABC family ATPase (NCBI ptt file)||26, 272|
|CAC0132||CAC0132||Hypothetical protein (NCBI ptt file)||247, 270|
|CAC0328||CAC0328||Predicted metal-dependent hydrolase (NCBI ptt file)||72, 272|
|CAC0514||CAC0514||CBS domain, similar to B.subtilis ytoI (NCBI ptt file)||64, 272|
|CAC0619||CAC0619||Nitrate ABC transporter ATP binding protein (NCBI ptt file)||190, 270|
|CAC0707||rpoN||RNA polymerase sigma-54 factor (NCBI ptt file)||170, 272|
|CAC0886||CAC0886||Hypothetical protein (NCBI ptt file)||207, 270|
|CAC0925||CAC0925||TPR-repeat-containing protein (NCBI ptt file)||53, 270|
|CAC0926||CAC0926||TPR-repeat-containing protein (NCBI ptt file)||123, 270|
|CAC1087||CAC1087||Hypothetical protein (NCBI ptt file)||139, 272|
|CAC1134||CAC1134||Phage related protein, YonF B.subtilis homolog (NCBI ptt file)||195, 272|
|CAC1137||CAC1137||Hypothetical protein (NCBI ptt file)||30, 272|
|CAC1321||glpK||Glycerol kinase, GLPK (NCBI ptt file)||272, 342|
|CAC1414||CAC1414||TerE family protein, ortholog of stress responce protein SCP2 (YCEC) B.subtilis (NCBI ptt file)||272, 298|
|CAC1418||CAC1418||Nitroreductase family protein (NCBI ptt file)||57, 272|
|CAC1442||CAC1442||Hypothetical protein (NCBI ptt file)||270, 317|
|CAC1446||CAC1446||Hypothetical protein (NCBI ptt file)||123, 270|
|CAC1477||CAC1477||Hypothetical protein (NCBI ptt file)||272, 301|
|CAC1650||CAC1650||Hypothetical protein, CF-38 family (NCBI ptt file)||123, 270|
|CAC1659||CAC1659||Predicted membrane protein (NCBI ptt file)||270, 282|
|CAC1741||CAC1741||Uncharacterized conserved protein, YLBM B.subtilis ortholog (NCBI ptt file)||151, 270|
|CAC1763||CAC1763||Predicted endonuclease (NCBI ptt file)||166, 270|
|CAC1849||CAC1849||Predicted flavoprotein, YhiN family (NCBI ptt file)||64, 272|
|CAC1947||CAC1947||Phage related transcriptional regulator (Xre family) (NCBI ptt file)||270, 272|
|CAC2027||CAC2027||Hypothetical protein (NCBI ptt file)||270, 328|
|CAC2030||CAC2030||Hypothetical protein (NCBI ptt file)||270, 281|
|CAC2054||CAC2054||Hypothetical protein (NCBI ptt file)||270, 313|
|CAC2079||CAC2079||Hypothetical protein (NCBI ptt file)||86, 272|
|CAC2097||CAC2097||Hypothetical protein (NCBI ptt file)||270, 317|
|CAC2099||CAC2099||Hypothetical protein (NCBI ptt file)||270, 320|
|CAC2114||CAC2114||Predicted pseudouridylate synthase, YLYB B.subtilis ortholog (NCBI ptt file)||26, 270|
|CAC2247||CAC2247||Site-specific recombinase, DNA invertase Pin homolog (NCBI ptt file)||270, 301|
|CAC2259||CAC2259||Predicted transcriptional regulator of MarR-family (NCBI ptt file)||270, 351|
|CAC2474||def||N-formylmethionyl-tRNA deformylase (NCBI ptt file)||57, 272|
|CAC2492||CAC2492||Predicted membrane, YNAG B.subtilis ortholog (NCBI ptt file)||270, 294|
|CAC2511||CAC2511||Predicted membrane protein (NCBI ptt file)||272, 320|
|CAC2512||CAC2512||Hypothetical protein (NCBI ptt file)||133, 270|
|CAC2609||CAC2609||Cytidine deaminase family enzyme (NCBI ptt file)||270, 320|
|CAC2668||CAC2668||Hypothetical protein (NCBI ptt file)||270, 317|
|CAC2805||CAC2805||Possible selenocysteine lyase (aminotransferase of NifS family) (NCBI ptt file)||148, 272|
|CAC2835||gntP||Gluconate permease, gntP (NCBI ptt file)||270, 288|
|CAC2918||pmi||Mannose-6 phospate isomelase (NCBI ptt file)||270, 360|
|CAC3045||CAC3045||CPSB/CAPC ortholog, PHP family hydrolase (NCBI ptt file)||272, 333|
|CAC3567||topB||Topoisomerase B (NCBI ptt file)||66, 270|
|CAC3628||oppF||Oligopeptide ABC transporter, ATPase component (NCBI ptt file)||270, 294|
|CAC3629||oppD||Oligopeptide ABC transporter, ATPase component (NCBI ptt file)||270, 294|
|CAC3658||CAC3658||Uncharacterized conserved membrane protein, SapB/MtgC family (NCBI ptt file)||41, 272|
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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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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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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