Organism : Clostridium acetobutylicum | Module List :
Phage related transcriptional regulator (Xre family) (NCBI ptt file)
Functional Annotations (1)
|sequence-specific DNA binding||go/ molecular_function|
Regulation information for CAC1946(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 CAC1946
|sequence-specific DNA binding||go/ molecular_function|
Module neighborhood information for CAC1946
|Gene||Common Name||Description||Module membership|
|CAC0249||CAC0249||Glyoxalase I (glyoxalase family) (NCBI ptt file)||102, 332|
|CAC0382||levR||Possible transcriptional regulator of levanase operon, AAA-ATPase domain (NtrC family), fused to 2 BglG-like domains, ortholog of B.subtilis levR (NCBI ptt file)||324, 332|
|CAC0743||CAC0743||6-phospho-beta-glucosidase (NCBI ptt file)||172, 332|
|CAC1660||CAC1660||Butyrate kinase, buk (NCBI ptt file)||332, 359|
|CAC1676||CAC1676||Uncharacterized conserved protein (NCBI ptt file)||301, 332|
|CAC1871||CAC1871||FtsK-like DNA segregation ATPase, YDCQ B.subtilis ortholog (NCBI ptt file)||332, 342|
|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|
|CAC1892||CAC1892||Hypothetical protein (NCBI ptt file)||180, 332|
|CAC1893||CAC1893||ClpP family serine protease, possible phage related (NCBI ptt file)||180, 332|
|CAC1894||CAC1894||Phage-related, head portal protein (NCBI ptt file)||180, 332|
|CAC1895||CAC1895||Phage terminase-like protein, large subunit (NCBI ptt file)||54, 332|
|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|
|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|
|CAC1916||CAC1916||Hypothetical protein (NCBI ptt file)||54, 332|
|CAC1918||CAC1918||Hypothetical protein (NCBI ptt file)||54, 332|
|CAC1944||CAC1944||Hypothetical protein (NCBI ptt file)||54, 332|
|CAC1946||CAC1946||Phage related transcriptional regulator (Xre family) (NCBI ptt file)||121, 332|
|CAC1951||CAC1951||Site-specific recombinases, DNA invertase Pin homolog (NCBI ptt file)||44, 332|
|CAC2669||CAC2669||Glu-tRNAGln amidotransferase subunit B (NCBI ptt file)||79, 332|
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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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.
- 2. Source gene
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