Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC1973(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 CAC1973
|Gene||Common Name||Description||Module membership|
|CAC0006||gyrB||DNA gyrase (topoisomerase II) B subunit (NCBI ptt file)||57, 64|
|CAC0084||CAC0084||MutT/Nudix family hydrolase (NCBI ptt file)||167, 322|
|CAC0225||CAC0225||Sensory transduction histidine kinase (NCBI ptt file)||57, 109|
|CAC0228||CAC0228||Hypothetical protein (NCBI ptt file)||304, 322|
|CAC0314||CAC0314||Uncharacterized protein homolog YKRK B. subtilis (NCBI ptt file)||57, 207|
|CAC0464||CAC0464||Protein, related to divalent cations, tolerance CutA family (NCBI ptt file)||167, 322|
|CAC0604||CAC0604||Acyl carrier protein phosphodiesterase (NCBI ptt file)||57, 279|
|CAC0751||CAC0751||Permease (NCBI ptt file)||322, 348|
|CAC0763||CAC0763||Transcriptional regulator, MarR family (NCBI ptt file)||132, 322|
|CAC0870||CAC0870||Hypothetical protein (NCBI ptt file)||242, 322|
|CAC1007||CAC1007||Predicted acetyltransferase (NCBI ptt file)||167, 322|
|CAC1022||CAC1022||Thioesterase II of alpha/beta hydrolase superfamily (NCBI ptt file)||166, 322|
|CAC1418||CAC1418||Nitroreductase family protein (NCBI ptt file)||57, 272|
|CAC1584||CAC1584||Metal-dependent hydrolase of the beta-lactamase superfamily (NCBI ptt file)||77, 322|
|CAC1599||CAC1599||Predicted membrane protein (NCBI ptt file)||252, 322|
|CAC1857||CAC1857||Predicted metal-dependent peptidase (NCBI ptt file)||57, 64|
|CAC1859||CAC1859||Hypothetical protein (NCBI ptt file)||57, 64|
|CAC1955||CAC1955||Hypothetical protein (NCBI ptt file)||57, 109|
|CAC1973||CAC1973||Hypothetical secreted protein (NCBI ptt file)||57, 322|
|CAC2063||dacF||D-alanyl-D-alanine carboxypeptidase (NCBI ptt file)||57, 64|
|CAC2141||CAC2141||Hypothetical protein (NCBI ptt file)||57, 273|
|CAC2310||CAC2310||Methenyl tetrahydrofolate cyclohydrolase (serine cycle enzyme) (NCBI ptt file)||57, 294|
|CAC2466||CAC2466||Predicted aldoketomutase of glyoxalase I family (NCBI ptt file)||162, 322|
|CAC2474||def||N-formylmethionyl-tRNA deformylase (NCBI ptt file)||57, 272|
|CAC2878||CAC2878||ABC-type iron (III) transport system, permease component (NCBI ptt file)||69, 322|
|CAC2950||lacR||Lactose phosphotransferase system repressor lacR (NCBI ptt file)||57, 146|
|CAC2987||CAC2987||Primase-like protein, containing TOPRIM domain, YABF B.subtilis ortholog (NCBI ptt file)||57, 273|
|CAC3072||CAC3072||Mannose-1-phosphate guanylyltransferase (NCBI ptt file)||57, 286|
|CAC3084||CAC3084||TPR-repeat-containing protein (NCBI ptt file)||167, 322|
|CAC3395||CAC3395||Predicted membrane protein (NCBI ptt file)||57, 86|
|CAC3396||CAC3396||Nudix (MutT) family hydrolase, C4-type Zn-finger domain containing (NCBI ptt file)||57, 322|
|CAC3502||CAC3502||Transcriptional regulator, fadR family (NCBI ptt file)||57, 206|
|CAC3553||CAC3553||Transcriptional regulator (LacI family) (NCBI ptt file)||224, 322|
|CAC3597||CAC3597||Rubrerythrin (NCBI ptt file)||4, 57|
|CAC3598||CAC3598||Rubrerythrin (NCBI ptt file)||4, 57|
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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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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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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