Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC2946(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 CAC2946
|Gene||Common Name||Description||Module membership|
|CAC0092||CAC0092||Uncharacterized predicted membrane protein, YTWI B.subtilis ortholog (NCBI ptt file)||305, 363|
|CAC0144||sfsa||Sugar fermentation-stimulation protein (NCBI ptt file)||154, 363|
|CAC0148||CAC0148||Predicted enzyme with TIM-barrel fold (NCBI ptt file)||117, 345|
|CAC0160||CAC0160||Predicted acetyltransferase (NCBI ptt file)||185, 345|
|CAC0177||appB||Oligopeptide transport permease protein (NCBI ptt file)||314, 345|
|CAC0280||CAC0280||Molybdate transport system, permease component (NCBI ptt file)||317, 363|
|CAC0281||CAC0281||Molybdate-binding periplasmic protein (NCBI ptt file)||363, 366|
|CAC0297||CAC0297||Lysine decarboxylase (NCBI ptt file)||73, 363|
|CAC0352||CAC0352||Uncharacterized conserved membrane protein, SANA family (NCBI ptt file)||115, 345|
|CAC0480||nrdD||Oxygen-sensitive ribonucleoside-triphosphate reductase nrdD (NCBI ptt file)||73, 363|
|CAC0713||eno||Enolase (NCBI ptt file)||128, 363|
|CAC0715||vacB||FUSION ribonuclease and ribosomal protein S1 domain (NCBI ptt file)||313, 363|
|CAC0746||CAC0746||Secreted protease metal-dependent protease (NCBI ptt file)||269, 345|
|CAC0845||CAC0845||Ferritin-like protein Rsg (NCBI ptt file)||65, 363|
|CAC0994||CAC0994||Predicted membrane protein (NCBI ptt file)||100, 345|
|CAC0995||CAC0995||Predicted membrane protein (NCBI ptt file)||80, 345|
|CAC1160||CAC1160||Hypothetical protein (NCBI ptt file)||25, 345|
|CAC1266||CAC1266||Pseudouridylate synthase family protein, yabo B.subtilis ortholog (NCBI ptt file)||67, 345|
|CAC1304||CAC1304||Uncharacterized conserved protein, predicted metal-binding (NCBI ptt file)||113, 363|
|CAC1324||CAC1324||Uncharacterized predected metal-binding protein (NCBI ptt file)||204, 363|
|CAC1426||CAC1426||Possible transcriptional regulator from leucine-rich protein (LRPR) family (NCBI ptt file)||47, 363|
|CAC1450||CAC1450||Predicted alpha/beta superfamily hydrolase (NCBI ptt file)||294, 345|
|CAC1592||CAC1592||Predicted permease, YCGR B.subtilis ortholog (NCBI ptt file)||69, 345|
|CAC1791||CAC1791||Undecaprenyl pyrophosphate synthase (NCBI ptt file)||282, 345|
|CAC1911||CAC1911||Hypothetical protein (NCBI ptt file)||117, 345|
|CAC1950||CAC1950||Hypothetical protein (NCBI ptt file)||117, 345|
|CAC1979||CAC1979||Predicted membrane protein (NCBI ptt file)||113, 363|
|CAC2055||CAC2055||Predicted transcriptional regulator (NCBI ptt file)||158, 345|
|CAC2168||CAC2168||Uncharacterized conserved protein (NCBI ptt file)||258, 345|
|CAC2233||CAC2233||TRNA 5-methylaminomethyl-2-thiouridylate)-methyltransferase, PP-loop ATPase (NCBI ptt file)||329, 363|
|CAC2287||CAC2287||Acyl-CoA reductase LuxC (NCBI ptt file)||73, 345|
|CAC2298||CAC2298||Predicted nucleotidyltransferase (NCBI ptt file)||91, 345|
|CAC2301||mrcB||Membrane carboxypeptidase mrcB (NCBI ptt file)||239, 345|
|CAC2343||CAC2343||LPS biosynthesis O-acetyl transferase (NCBI ptt file)||100, 345|
|CAC2414||CAC2414||Uncharacterized conserved protein, related to alpha-amylase/alpha-mannosidase (NCBI ptt file)||283, 345|
|CAC2543||etfA||Electron-transferring flavoprotein large subunit (NCBI ptt file)||41, 363|
|CAC2660||pykA||Pyruvate carboxylase, PYKA (NCBI ptt file)||29, 345|
|CAC2687||recQ||RecQ protein, superfamily II DNA helicase (NCBI ptt file)||113, 345|
|CAC2694||CAC2694||Hypothetical protein (NCBI ptt file)||158, 345|
|CAC2781||CAC2781||Hypothetical protein (NCBI ptt file)||62, 345|
|CAC2921||thiH||Thiamine biosynthesis enzyme, thiH (NCBI ptt file)||208, 363|
|CAC2923||CAC2923||Dinucleotide-utilizing enzyme involved in molybdopterin/thiamine biosynthesis (NCBI ptt file)||208, 363|
|CAC2945||CAC2945||Possible phosphoglycerate dehydrogenase (NCBI ptt file)||279, 363|
|CAC2946||CAC2946||Hypothetical protein (NCBI ptt file)||345, 363|
|CAC2961||galT||Galactose-1-phosphate uridyltransferase (NCBI ptt file)||75, 345|
|CAC2977||gatA||Glutamyl-tRNAGln amidotransferase subunit A (NCBI ptt file)||221, 363|
|CAC2988||CAC2988||Uncharacterized conserved protein, YABE B.subtilis ortholog (NCBI ptt file)||267, 345|
|CAC3424||CAC3424||Transcriptional regulator, RpiR family (NCBI ptt file)||158, 345|
|CAC3648||CAC3648||Acetyltransferase (with duplicated domains), possibly RIMI-like protein (NCBI ptt file)||73, 363|
|CAC3652||alsS||Acetolactate synthase (NCBI ptt file)||47, 363|
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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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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