Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC1905(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 CAC1905
|Gene||Common Name||Description||Module membership|
|CAC0261||nifV||Homocitrate synthase,alpha subunit nifV(nioA) (NCBI ptt file)||171, 220|
|CAC0370||CAC0370||Cation efflux system protein, AcrB/AcrF/AcrD family (NCBI ptt file)||171, 307|
|CAC0373||CAC0373||ABC transporter, ATP binding protein (NCBI ptt file)||171, 241|
|CAC0446||CAC0446||Hydrolase of MutT (Nudix) family (NCBI ptt file)||171, 226|
|CAC0645||CAC0645||Similar to spore germination protein (NCBI ptt file)||171, 220|
|CAC1862||CAC1862||Hypothetical protein (NCBI ptt file)||171, 307|
|CAC1875||CAC1875||Hypothetical protein, CF-36 family (NCBI ptt file)||121, 180|
|CAC1876||lyc||N-acetylmuramidase, autolytic enzyme, family 25 of glycosyl hydrolases ; peptodoglycan-binding domain (NCBI ptt file)||121, 180|
|CAC1877||CAC1877||Hypothetical protein, CF-8 family (NCBI ptt file)||121, 180|
|CAC1878||CAC1878||Hypothetical protein (NCBI ptt file)||121, 180|
|CAC1879||CAC1879||Uncharacterized, phage-related protein (NCBI ptt file)||121, 180|
|CAC1880||CAC1880||Hypothetical protein, CF-35 family (NCBI ptt file)||121, 180|
|CAC1881||CAC1881||Hypothetical protein (NCBI ptt file)||121, 332|
|CAC1882||CAC1882||Hypothetical protein (NCBI ptt file)||121, 180|
|CAC1883||CAC1883||Uncharacterized phage related protein (NCBI ptt file)||121, 180|
|CAC1884||CAC1884||Hypothetical protein (NCBI ptt file)||121, 180|
|CAC1885||CAC1885||Hypothetical protein (NCBI ptt file)||121, 180|
|CAC1886||CAC1886||Uncharacterized phage related protein (NCBI ptt file)||121, 180|
|CAC1887||CAC1887||Hypothetical protein (NCBI ptt file)||121, 180|
|CAC1888||CAC1888||Uncharacterized phage related protein (NCBI ptt file)||121, 180|
|CAC1889||CAC1889||Uncharacterized phage related protein (NCBI ptt file)||121, 180|
|CAC1890||CAC1890||Phage related protein, possible DNA packing (NCBI ptt file)||121, 180|
|CAC1896||CAC1896||Phage terminase-like protein, small subunit (NCBI ptt file)||121, 180|
|CAC1897||CAC1897||Phage-related, Zn finger domain containing protein (NCBI ptt file)||121, 180|
|CAC1898||CAC1898||Hypothetical protein (NCBI ptt file)||121, 180|
|CAC1899||CAC1899||Hypothetical protein (NCBI ptt file)||121, 180|
|CAC1900||CAC1900||Phage regulatory Com-like protein, containing Zn-finger (NCBI ptt file)||54, 171|
|CAC1902||CAC1902||Hypothetical protein (NCBI ptt file)||121, 180|
|CAC1903||CAC1903||Hypothetical protein (NCBI ptt file)||121, 180|
|CAC1904||CAC1904||Hypothetical protein (NCBI ptt file)||121, 180|
|CAC1905||CAC1905||Hypothetical protein (NCBI ptt file)||121, 171|
|CAC1906||CAC1906||Hypothetical protein (NCBI ptt file)||121, 180|
|CAC1907||CAC1907||Hypothetical protein (NCBI ptt file)||121, 180|
|CAC1908||CAC1908||Predicted membrane protein (NCBI ptt file)||121, 180|
|CAC1912||CAC1912||Uncharacterized phage related protein (NCBI ptt file)||121, 366|
|CAC1913||CAC1913||Zn-finger containing protein (NCBI ptt file)||121, 180|
|CAC1945||CAC1945||Phage related anti-repressor protein (NCBI ptt file)||54, 171|
|CAC1946||CAC1946||Phage related transcriptional regulator (Xre family) (NCBI ptt file)||121, 332|
|CAC2534||CAC2534||HD_GYP hydrolase domain fused to HD hydrolase domain (NCBI ptt file)||171, 220|
|CAC2618||CAC2618||Hypothetical protein, CF-17 family (NCBI ptt file)||171, 220|
|CAC3358||CAC3358||Site-specific DNA methylase dam (NCBI ptt file)||125, 171|
|CAC3367||CAC3367||Protein distantly similar to N-terminal fragment of HSP60 chaperonin family (NCBI ptt file)||125, 171|
|CAC3462||fabG||3-oxoacyl-acyl carrier protein reductase (NCBI ptt file)||171, 220|
|CAC3513||CAC3513||Hypothetical protein (NCBI ptt file)||171, 220|
|CAC3564||aspC||aspartyl-tRNA synthetase (RefSeq)||171, 220|
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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Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.
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;
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