Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC2923(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 CAC2923
Module neighborhood information for CAC2923
|Gene||Common Name||Description||Module membership|
|CAC0041||CAC0041||Uncharacterized small conserved protein, homolog of yfjA/yukE B.subtilis (NCBI ptt file)||208, 264|
|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|
|CAC0227||CAC0227||Predicted permease (NCBI ptt file)||169, 208|
|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|
|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|
|CAC0845||CAC0845||Ferritin-like protein Rsg (NCBI ptt file)||65, 363|
|CAC1094||CAC1094||Cation efflux system protein (NCBI ptt file)||208, 320|
|CAC1247||pbpA||Penicillin-binding protein 2 (NCBI ptt file)||144, 208|
|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|
|CAC1387||CAC1387||Membrane associated chemotaxis sensory transducer protein (MSP domain and HAMP domain) (NCBI ptt file)||100, 208|
|CAC1426||CAC1426||Possible transcriptional regulator from leucine-rich protein (LRPR) family (NCBI ptt file)||47, 363|
|CAC1513||asrA||Anaerobic sulfite reductase (Fe-S subunit) (NCBI ptt file)||208, 240|
|CAC1521||CAC1521||Uncharacterized membrane protein, yetF/ydfS/ykjA/yrbG/ydfR B.subtilis ortholog (NCBI ptt file)||150, 208|
|CAC1702||CAC1702||Hypothetical protein (NCBI ptt file)||208, 336|
|CAC1959||CAC1959||Uncharacterized protein, YYAC B.subtilis homolog (fragment) (NCBI ptt file)||190, 208|
|CAC1960||CAC1960||Uncharacterized protein, YYAC B.subtilis homolog (NCBI ptt file)||208, 336|
|CAC1974||CAC1974||Hypothetical secreted protein (NCBI ptt file)||208, 336|
|CAC1979||CAC1979||Predicted membrane protein (NCBI ptt file)||113, 363|
|CAC1981||CAC1981||Hypothetical protein (NCBI ptt file)||208, 336|
|CAC2028||CAC2028||Hypothetical protein, CF-4 family (NCBI ptt file)||205, 208|
|CAC2046||CAC2046||Predicted membrane protein (NCBI ptt file)||208, 336|
|CAC2048||CAC2048||Uncharacterized secreted protein (NCBI ptt file)||208, 336|
|CAC2049||CAC2049||Predicted membrane protein (NCBI ptt file)||208, 336|
|CAC2233||CAC2233||TRNA 5-methylaminomethyl-2-thiouridylate)-methyltransferase, PP-loop ATPase (NCBI ptt file)||329, 363|
|CAC2493||CAC2493||Phospholipase C family protein (NCBI ptt file)||205, 208|
|CAC2503||CAC2503||Hypothetical protein (NCBI ptt file)||65, 208|
|CAC2543||etfA||Electron-transferring flavoprotein large subunit (NCBI ptt file)||41, 363|
|CAC2745||CAC2745||Membrane associated methyl-accepting chemotaxis protein (NCBI ptt file)||208, 236|
|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|
|CAC2924||thiS||Uncharacterized protein, possibly involved in thiamine biosynthesis (NCBI ptt file)||208, 336|
|CAC2945||CAC2945||Possible phosphoglycerate dehydrogenase (NCBI ptt file)||279, 363|
|CAC2946||CAC2946||Hypothetical protein (NCBI ptt file)||345, 363|
|CAC2977||gatA||Glutamyl-tRNAGln amidotransferase subunit A (NCBI ptt file)||221, 363|
|CAC3415||CAC3415||ABC-type multidrug/protein/lipid transport system, ATPase component (NCBI ptt file)||123, 208|
|CAC3476||CAC3476||Methyl-accepting chemotaxis protein (NCBI ptt file)||208, 353|
|CAC3488||CAC3488||Predicted transcriptional regulator (NCBI ptt file)||69, 208|
|CAC3554||CAC3554||Siderophore/Surfactin synthetase related protein (NCBI ptt file)||26, 208|
|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.
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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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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