Organism : Clostridium acetobutylicum | Module List :
Possible 3-oxoacyl-[acyl-carrier-protein] synthase III (NCBI ptt file)
Functional Annotations (1)
|3-oxoacyl-[acyl-carrier-protein] synthase III||cog/ cog|
Regulation information for CAC2011(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 2 motifs predicted.
|Motif Id||e-value||Consensus||Motif Logo|
Functional Enrichment for CAC2011
|3-oxoacyl-[acyl-carrier-protein] synthase III||cog/ cog|
Module neighborhood information for CAC2011
|Gene||Common Name||Description||Module membership|
|CAC0815||CAC0815||Methyl-accepting chemotaxis protein (NCBI ptt file)||134, 209|
|CAC0816||CAC0816||Lipase-esterase related protein (NCBI ptt file)||176, 209|
|CAC0869||CAC0869||Thioredoxine reductase (NCBI ptt file)||31, 209|
|CAC0982||CAC0982||Hypothetical protein (NCBI ptt file)||209, 266|
|CAC1669||CstA||Carbon starvation protein (NCBI ptt file)||209, 238|
|CAC1764||CAC1764||Predicted glutamine amidotransferase (NCBI ptt file)||31, 209|
|CAC1854||CAC1854||Nudix (MutT) family hydrolase (NCBI ptt file)||209, 277|
|CAC1988||CAC1988||Ferrichrome-binding periplasmic protein (NCBI ptt file)||68, 97|
|CAC1993||moaA||Molybdenum cofactor biosynthesis enzyme MoaA, Fe-S oxidoreductase (NCBI ptt file)||97, 294|
|CAC1996||CAC1996||Hypothetical protein (NCBI ptt file)||68, 97|
|CAC1997||CAC1997||Predicted glycosyltransferase (NCBI ptt file)||68, 97|
|CAC1998||CAC1998||ABC-type transport system, ATPase component (NCBI ptt file)||68, 97|
|CAC1999||CAC1999||Uncharacterized protein related to hypothetical protein Cj1507c from Campylobacter jejuni (NCBI ptt file)||97, 294|
|CAC2001||iorA||Indolepyruvate ferredoxin oxidoreductase, subunit alpha (NCBI ptt file)||97, 166|
|CAC2002||CAC2002||Predicted iron-sulfur flavoprotein (NCBI ptt file)||68, 97|
|CAC2003||CAC2003||Predicted permease (NCBI ptt file)||97, 166|
|CAC2004||CAC2004||Siderophore/Surfactin synthetase related protein (NCBI ptt file)||60, 209|
|CAC2005||CAC2005||Siderophore/Surfactin synthetase related protein (NCBI ptt file)||97, 166|
|CAC2006||CAC2006||Enzyme of siderophore/surfactin biosynthesis (NCBI ptt file)||68, 97|
|CAC2007||CAC2007||Predicted glycosyltransferase (NCBI ptt file)||97, 209|
|CAC2008||pksF||3-oxoacyl-(acyl-carrier-protein) synthase (NCBI ptt file)||68, 97|
|CAC2009||mmgB||3-Hydroxyacyl-CoA dehydrogenase (NCBI ptt file)||97, 166|
|CAC2010||CAC2010||Predicted Fe-S oxidoreductase (NCBI ptt file)||97, 166|
|CAC2011||fabH||Possible 3-oxoacyl-[acyl-carrier-protein] synthase III (NCBI ptt file)||97, 209|
|CAC2012||fadB||Enoyl-CoA hydratase (NCBI ptt file)||97, 294|
|CAC2013||CAC2013||Hypothetical protein (NCBI ptt file)||53, 97|
|CAC2014||CAC2014||Predicted esterase (NCBI ptt file)||97, 166|
|CAC2015||CAC2015||Hypothetical protein (NCBI ptt file)||53, 97|
|CAC2016||fadB||Enoyl-CoA hydratase (NCBI ptt file)||97, 209|
|CAC2017||CAC2017||Acyl carrier protein (NCBI ptt file)||134, 209|
|CAC2018||CAC2018||Aldehyde:ferredoxin oxidoreductase (NCBI ptt file)||134, 209|
|CAC2021||moeA||Molybdopterin biosynthesis enzyme, MoeA (short form) (NCBI ptt file)||133, 209|
|CAC2022||moaB||Molybdopterin biosynthesis enzyme, moaB (NCBI ptt file)||209, 282|
|CAC2025||CAC2025||Hypothetical protein (NCBI ptt file)||209, 282|
|CAC2182||CAC2182||Hypothetical protein (NCBI ptt file)||209, 348|
|CAC2446||CAC2446||Hypothetical protein (NCBI ptt file)||27, 209|
|CAC3037||ccpA||Catabolite control protein, LacI family transcriptional regulator (NCBI ptt file)||11, 209|
|CAC3279||CAC3279||Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats (NCBI ptt file)||209, 261|
|CAC3290||CAC3290||Iron-regulated ABC-type transporter membrane component (SufB) (NCBI ptt file)||201, 209|
|CAC3291||CAC3291||Selenocysteine lyase, NifS family (NCBI ptt file)||209, 296|
|CAC3292||CAC3292||NifU homolog involved in Fe-S cluster formation (NCBI ptt file)||209, 277|
|CAC3592||CAC3592||Hypothetical protein, CF-27 family (NCBI ptt file)||92, 209|
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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Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.
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
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