Organism : Clostridium acetobutylicum | Module List :
DnaK protein (heat shock protein), C-terminal region has VWA type A domain (NCBI ptt file)
Functional Annotations (4)
|Molecular chaperone||cog/ cog|
|cell morphogenesis||go/ biological_process|
|ATP binding||go/ molecular_function|
|2-alkenal reductase [NAD(P)] activity||go/ molecular_function|
Regulation information for CAC0473(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 CAC0473
Module neighborhood information for CAC0473
|Gene||Common Name||Description||Module membership|
|CAC0441||CAC0441||Uncharacterized conserved membrane protein of SANA family (NCBI ptt file)||14, 44|
|CAC0472||dnaK||DnaK protein (heat shock protein), HSP70/DnaK family (NCBI ptt file)||14, 271|
|CAC0473||dnaK||DnaK protein (heat shock protein), C-terminal region has VWA type A domain (NCBI ptt file)||14, 41|
|CAC0512||CAC0512||Uncharacterized conserved protein, YbhK/UPF0052 family (NCBI ptt file)||41, 343|
|CAC0513||CAC0513||Uncharacterized conserved protein, similar to B.subtilis yvcL (NCBI ptt file)||41, 154|
|CAC0531||CAC0531||Transcriptional regulator, RpiR family (NCBI ptt file)||41, 64|
|CAC0566||CAC0566||Malate dehydrogenase (NCBI ptt file)||14, 22|
|CAC0821||CAC0821||Transcriptional regulator (TetR/AcrR family) (NCBI ptt file)||14, 271|
|CAC0823||CAC0823||Predicted membrane protein (NCBI ptt file)||14, 271|
|CAC0959||clpB||ATPase with chaperone activity, two ATP-binding domains (NCBI ptt file)||6, 41|
|CAC1474||CAC1474||Proline/glycine betaine ABC transport system, periplasmic component (NCBI ptt file)||41, 177|
|CAC1475||CAC1475||Proline/glycine betaine ABC transport system, ATPase component (NCBI ptt file)||41, 177|
|CAC1553||CAC1553||Membrane associated sensory transduction histidine kinase (with HAMP domain) (NCBI ptt file)||41, 265|
|CAC1665||CAC1665||Predicted amidohydrolase (NCBI ptt file)||41, 113|
|CAC1699||CAC1699||Uncharacterized protein, YfiH family (NCBI ptt file)||14, 172|
|CAC1700||CAC1700||Response regulator (CheY-like receiver domain and DNA-binding HTH domain) (NCBI ptt file)||6, 14|
|CAC1767||CAC1767||Hypothetical protein (NCBI ptt file)||14, 22|
|CAC1802||infB||Translation IF2, GTPase (NCBI ptt file)||14, 213|
|CAC1964||rpsA||Ribosomal protein S1 (NCBI ptt file)||41, 47|
|CAC2052||CAC2052||DNA-dependent RNA polymerase sigma subunit (NCBI ptt file)||41, 64|
|CAC2053||CAC2053||Hypothetical protein (NCBI ptt file)||41, 64|
|CAC2142||CAC2142||Hypothetical protein (NCBI ptt file)||6, 14|
|CAC2143||sigD||Sigma factor of SigD/WhiG family (NCBI ptt file)||14, 41|
|CAC2144||CAC2144||Uncharacterized protein, YPFA B.subtilis ortholog (NCBI ptt file)||14, 41|
|CAC2145||CAC2145||ATPases involved in chromosome partitioning, MinD family, YLXH B.subtilis ortholog (NCBI ptt file)||14, 41|
|CAC2146||flhF||Flagellar GTP-binding protein, FlhF (NCBI ptt file)||6, 14|
|CAC2262||addA||ATP-dependent exonuclease (exonuclease V) synthesis protein AddA (helicase and exonuclease domains) (NCBI ptt file)||14, 159|
|CAC2354||CAC2354||Nifs family aminotransferase (NCBI ptt file)||41, 279|
|CAC2458||CAC2458||2-oxoacid ferredoxin oxidoreductase, beta subunit (NCBI ptt file)||41, 200|
|CAC2542||CAC2542||FAD/FMN-containing dehydrogenase (NCBI ptt file)||41, 265|
|CAC2543||etfA||Electron-transferring flavoprotein large subunit (NCBI ptt file)||41, 363|
|CAC2544||etfB||Electron-transferring flavoprotein small subunit (NCBI ptt file)||41, 291|
|CAC2625||CAC2625||Predicted membrane protein (NCBI ptt file)||41, 113|
|CAC2638||lonB||Lon-like ATP-dependent protease (NCBI ptt file)||41, 177|
|CAC2685||CAC2685||Trehalose/maltose hydrolase (phosphorylase) (NCBI ptt file)||6, 14|
|CAC3030||CAC3030||Hypothetical protein (NCBI ptt file)||41, 265|
|CAC3080||CAC3080||Hypothetical protein (NCBI ptt file)||39, 41|
|CAC3475||CAC3475||Transcriptional regulator, merR family (NCBI ptt file)||14, 320|
|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.
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