Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC0133(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 CAC0133
|Gene||Common Name||Description||Module membership|
|CAC0075||CAC0075||Ferredoxin (NCBI ptt file)||69, 150|
|CAC0124||CAC0124||Hypothetical protein (NCBI ptt file)||108, 150|
|CAC0133||CAC0133||Hypothetical protein, CF-4 family (NCBI ptt file)||150, 300|
|CAC0206||CAC0206||Uncharacterized conserved membrane protein (NCBI ptt file)||98, 150|
|CAC0501||bacA||Bacitracin resistance protein (bacA) (NCBI ptt file)||69, 300|
|CAC0577||CAC0577||Endo-arabinase related enzyme (family 43 glycosyl hydrolase domain and ricin B-like domain) (NCBI ptt file)||150, 216|
|CAC0613||CAC0613||Spore coat protein F (NCBI ptt file)||203, 300|
|CAC0614||CAC0614||Spore coat protein F (NCBI ptt file)||203, 300|
|CAC0719||CAC0719||Epoxide hydrolase, similar to eukaryotic (NCBI ptt file)||150, 356|
|CAC0810||hypF||Hydrogenase maturation factor (hypF) (NCBI ptt file)||95, 300|
|CAC0813||CAC0813||Hypothetical protein (NCBI ptt file)||123, 150|
|CAC0863||CAC0863||Sensory transduction histidine kinase (NCBI ptt file)||39, 300|
|CAC0955||CAC0955||ATP-dependent Zn protease (NCBI ptt file)||150, 190|
|CAC1332||uxuA||D-mannonate hydrolase (NCBI ptt file)||150, 169|
|CAC1359||CAC1359||Predicted xylanase/chitin deacetylase (NCBI ptt file)||150, 190|
|CAC1423||CAC1423||Predicted dehydrogenase of short-chain alcohol dehydrogenase family, ortholog of YHDF B.subtilis (NCBI ptt file)||118, 300|
|CAC1458||CAC1458||PTS system, fructose(mannose)-specific IIB (NCBI ptt file)||136, 150|
|CAC1508||CAC1508||Hypothetical protein (NCBI ptt file)||39, 300|
|CAC1521||CAC1521||Uncharacterized membrane protein, yetF/ydfS/ykjA/yrbG/ydfR B.subtilis ortholog (NCBI ptt file)||150, 208|
|CAC1536||CAC1536||Transcriptional regulator, AcrR family (NCBI ptt file)||150, 165|
|CAC1839||CAC1839||Hypothetical protein (NCBI ptt file)||39, 300|
|CAC1985||CAC1985||Hypothetical protein (NCBI ptt file)||279, 300|
|CAC2249||CAC2249||C-terminal domain of asparagine synthase (NCBI ptt file)||114, 300|
|CAC2300||CAC2300||Uncharacterized secreted protein, YunB B.subtilis homolog (NCBI ptt file)||39, 300|
|CAC2438||CAC2438||Predicted phosphatase (NCBI ptt file)||174, 300|
|CAC2582||CAC2582||Uncharacterized conserved membrane protein, YHGE B.subtilis homolog (NCBI ptt file)||39, 300|
|CAC2583||CAC2583||Uncharacterized conserved membrane protein, YHGE B.subtilis homolog (NCBI ptt file)||150, 300|
|CAC2587||CAC2587||GGDEF domain containing protein (NCBI ptt file)||150, 169|
|CAC2588||CAC2588||Glycosyltransferase (NCBI ptt file)||150, 169|
|CAC2596||CAC2596||Rieske FeS-domain containing oxidoreductase (NCBI ptt file)||65, 150|
|CAC2600||CAC2600||Predicted membrane protein (NCBI ptt file)||300, 301|
|CAC2666||CAC2666||Hypothetical protein (NCBI ptt file)||300, 330|
|CAC2682||CAC2682||Hypothetical protein (NCBI ptt file)||62, 300|
|CAC2683||cotF||Related to spore coat protein F (NCBI ptt file)||62, 300|
|CAC2691||CAC2691||D-lactate dehydrogenase (NCBI ptt file)||150, 338|
|CAC2761||CAC2761||Thiamine biosynthesis lipoprotein ApbE (NCBI ptt file)||150, 183|
|CAC2762||CAC2762||Polyferredoxin (NCBI ptt file)||26, 150|
|CAC2790||CAC2790||Hypothetical protein (NCBI ptt file)||39, 300|
|CAC2794||CAC2794||Transcriptional regulator, Lrp family (possible nitrite reductase regulator NirD) (NCBI ptt file)||300, 330|
|CAC2796||CAC2796||MoaA/NirJ family Fe-S oxidoreductase (NCBI ptt file)||188, 300|
|CAC3015||CAC3015||Glycosyltransferase (NCBI ptt file)||39, 300|
|CAC3240||CAC3240||Predicted membrane protein (NCBI ptt file)||13, 150|
|CAC3241||CAC3241||Uncharacterized conserved membrane protein, YYAD B.subtilis ortholog (NCBI ptt file)||150, 301|
|CAC3330||CAC3330||Cytochrome P450 family protein, YBDT B.subtilis ortholog (NCBI ptt file)||154, 300|
|CAC3332||CAC3332||Predicted amidohydrolase (dihydroorothase family) (NCBI ptt file)||150, 360|
|CAC3346||CAC3346||MDR-type permease (NCBI ptt file)||4, 150|
|CAC3361||CAC3361||Transcriptional regulator, LysR family (NCBI ptt file)||150, 240|
|CAC3370||CAC3370||Predicted transcriptional regulator (NCBI ptt file)||150, 240|
|CAC3433||CAC3433||Transcriptional regulators, AcrR family (NCBI ptt file)||150, 344|
|CAC3546||CAC3546||Highly conserved protein containing a domain related to cellulase catalitic domain and a thioredoxin domain (NCBI ptt file)||259, 300|
|CAC3549||CAC3549||Subtilisin-like serine protease (NCBI ptt file)||150, 190|
|CAC3609||CAC3609||ABC-type MDR transport system, permease component (NCBI ptt file)||26, 150|
|CAC3610||CAC3610||ABC-type MDR transport system, permease component (NCBI ptt file)||24, 150|
|CAC3674||CAC3674||Two CBS domain containing protein (NCBI ptt file)||114, 300|
|CAC3697||CAC3697||Uncharacterized, Zn-finger domain containing protein, YXKC B.subtilis homolog (NCBI ptt file)||123, 150|
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.
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.
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;
- 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
- 3. Target genes (other module members)
- 4. Interactions between source and target genes for a particular module
- 5. Module(s) that source gene and target genes belong to
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