Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC1103(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 CAC1103
|Gene||Common Name||Description||Module membership|
|CAC0504||CAC0504||FHA-domain containing secreted protein (NCBI ptt file)||58, 268|
|CAC0555||CAC0555||Predicted membrane protein (NCBI ptt file)||7, 134|
|CAC0815||CAC0815||Methyl-accepting chemotaxis protein (NCBI ptt file)||134, 209|
|CAC0902||CAC0902||Predicted membrane protein (NCBI ptt file)||134, 277|
|CAC0903||CAC0903||Sensory transduction histidine kinase (NCBI ptt file)||134, 277|
|CAC0953||CAC0953||Hypothetical protein (NCBI ptt file)||25, 268|
|CAC0976||CAC0976||Uncharacterized conserved protein, ortholog yuzA B.subtilis (NCBI ptt file)||268, 295|
|CAC0977||asnC||Transcriptional regulator, Lrp family (NCBI ptt file)||152, 268|
|CAC0978||CAC0978||Possible elongation subunit of DNA-dependent DNA polymerase (NCBI ptt file)||5, 268|
|CAC0987||CAC0987||Hypothetical protein (NCBI ptt file)||38, 134|
|CAC0988||CAC0988||Probably membrane protein (NCBI ptt file)||5, 134|
|CAC0996||CAC0996||Hypothetical protein (NCBI ptt file)||25, 268|
|CAC1102||CAC1102||Predicted membrane protein (NCBI ptt file)||25, 268|
|CAC1103||CAC1103||Possible metal-binding domain, related to a correspondent domain of site-specific recombinase (NCBI ptt file)||134, 268|
|CAC1121||CAC1121||Predicted membrane protein (NCBI ptt file)||134, 152|
|CAC1169||CAC1169||Hypothetical protein (NCBI ptt file)||53, 134|
|CAC1214||CAC1214||Xre family DNA-binding domain and TPR-repeat containing protein (NCBI ptt file)||152, 268|
|CAC1480||CAC1480||Predicted dehydrogenase (NCBI ptt file)||113, 134|
|CAC1568||CAC1568||Diguanylate cyclase/phosphodiesterase domain 1 (GGDEF) (NCBI ptt file)||134, 162|
|CAC1587||CAC1587||Integral membrane protein possibly involved in chromosome condensation (NCBI ptt file)||134, 182|
|CAC1874||CAC1874||Hypothetical protein (NCBI ptt file)||25, 268|
|CAC2017||CAC2017||Acyl carrier protein (NCBI ptt file)||134, 209|
|CAC2018||CAC2018||Aldehyde:ferredoxin oxidoreductase (NCBI ptt file)||134, 209|
|CAC2024||CAC2024||Phosphatidylglycerophosphate synthase related protein (fragment) (NCBI ptt file)||25, 268|
|CAC2026||CAC2026||Predicted flavodoxin (NCBI ptt file)||25, 268|
|CAC2067||CAC2067||Hypothetical protein (NCBI ptt file)||51, 268|
|CAC2068||CAC2068||Sporulation factor spoIIM, uncharacterized membrane protein (NCBI ptt file)||51, 268|
|CAC2280||CAC2280||Predicted membrane protein (NCBI ptt file)||134, 268|
|CAC2505||CAC2505||Uncharacterized membrane protein, YXJN B.subtilis homolog (NCBI ptt file)||134, 176|
|CAC2518||CAC2518||Extracellular neutral metalloprotease, NPRE (fragment or C-term. domain) (NCBI ptt file)||134, 268|
|CAC2623||CAC2623||Possible sensorory transduction protein, containing AAA ATPase domain, TPR repeats domain, GGDEF domain and GAF domain (NCBI ptt file)||134, 269|
|CAC2784||CAC2784||Signal peptidase type IV (NCBI ptt file)||134, 277|
|CAC2785||CAC2785||Hypothetical protein (NCBI ptt file)||134, 225|
|CAC3023||CAC3023||Hypothetical protein (NCBI ptt file)||268, 292|
|CAC3417||CAC3417||Flavodoxin (NCBI ptt file)||25, 268|
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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