Organism : Clostridium acetobutylicum | Module List :
Membrane protease subunit, stomatin/prohibitin homolog (NCBI ptt file)
Functional Annotations (2)
|Membrane protease subunits, stomatin/prohibitin homologs||cog/ cog|
Regulation information for CAC1052(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 CAC1052
|Membrane protease subunits, stomatin/prohibitin homologs||cog/ cog|
Module neighborhood information for CAC1052
|Gene||Common Name||Description||Module membership|
|CAC0183||CAC0183||Transcriptional regulators of NagC/XylR (ROK) family, sugar kinase (NCBI ptt file)||6, 316|
|CAC0284||CAC0284||Transcriptional regulatory protein, Sir2 family (NCBI ptt file)||6, 343|
|CAC0312||CAC0312||Hypothetical protein (NCBI ptt file)||4, 172|
|CAC0313||CAC0313||Phage shock protein A (NCBI ptt file)||4, 172|
|CAC0318||CAC0318||Membrane permease, predicted cation efflux pumps (NCBI ptt file)||6, 338|
|CAC0319||CAC0319||ABC transporter ATP-binding protein (NCBI ptt file)||6, 342|
|CAC0368||CAC0368||4 animobutyrate aminotransferase (NCBI ptt file)||172, 271|
|CAC0377||CAC0377||Amino acid (glutamine) ABC transporter, permease component (NCBI ptt file)||172, 256|
|CAC0460||CAC0460||CBS-domain containing protein, YHDP B.subtilis ortholog (NCBI ptt file)||79, 172|
|CAC0649||CAC0649||Uncharacterized protein, homolog of Thermotoga maritima (4982386) (NCBI ptt file)||79, 172|
|CAC0743||CAC0743||6-phospho-beta-glucosidase (NCBI ptt file)||172, 332|
|CAC0959||clpB||ATPase with chaperone activity, two ATP-binding domains (NCBI ptt file)||6, 41|
|CAC1051||CAC1051||Uncharacterized conserved protein (possible membrane) (NCBI ptt file)||6, 172|
|CAC1052||CAC1052||Membrane protease subunit, stomatin/prohibitin homolog (NCBI ptt file)||6, 172|
|CAC1239||CAC1239||Predicted membrane protein (NCBI ptt file)||172, 281|
|CAC1260||obg||SPO0B-associated GTPase, obg (NCBI ptt file)||172, 256|
|CAC1261||CAC1261||Predicted RNA-binding protein containing KH domain (NCBI ptt file)||172, 256|
|CAC1545||deoC||Deoxyribose-phosphate aldolase (NCBI ptt file)||172, 200|
|CAC1699||CAC1699||Uncharacterized protein, YfiH family (NCBI ptt file)||14, 172|
|CAC1700||CAC1700||Response regulator (CheY-like receiver domain and DNA-binding HTH domain) (NCBI ptt file)||6, 14|
|CAC1719||rpoZ||RNA polymerase-associated protein RpoZ, omega subunit (YLOH B.subtilis ortholog) (NCBI ptt file)||172, 281|
|CAC1720||CAC1720||Flavoprotein involved in panthothenate metabolism, YLOI B.subtilis ortholog (NCBI ptt file)||8, 172|
|CAC1721||rpiA||Primosomal protein N', superfamily II helicase (NCBI ptt file)||172, 234|
|CAC1722||def||N-formylmethionyl-tRNA deformylase (NCBI ptt file)||6, 159|
|CAC1727||CAC1727||Protein serine/threonine phosphatases, PP2C family (YLOO B.subtilis ortholog) (NCBI ptt file)||6, 271|
|CAC1828||CAC1828||TldD protein fragment (NCBI ptt file)||159, 172|
|CAC1837||mutS||Mismatch repair protein MutS, ATPase (NCBI ptt file)||159, 172|
|CAC2142||CAC2142||Hypothetical protein (NCBI ptt file)||6, 14|
|CAC2146||flhF||Flagellar GTP-binding protein, FlhF (NCBI ptt file)||6, 14|
|CAC2333||spsI||DTDP-glucose pyrophosphorylase (NCBI ptt file)||26, 172|
|CAC2416||CAC2416||Uncharacterized protein, ErfK family; contains peptidoglycan-binding domain (NCBI ptt file)||6, 263|
|CAC2685||CAC2685||Trehalose/maltose hydrolase (phosphorylase) (NCBI ptt file)||6, 14|
|CAC2758||CAC2758||Uncharacterized protein, YPUA B.subtilis ortholog (NCBI ptt file)||79, 172|
|CAC2920||tenI||Thiamine monophosphate synthase (NCBI ptt file)||6, 316|
|CAC2922||thiG||Uncharacterized enzyme of thiazol biosynthesis (NCBI ptt file)||6, 316|
|CAC2975||CAC2975||Hypothetical protein (NCBI ptt file)||47, 172|
|CAC3189||clpC||ATPases with chaperone activity clpC, two ATP-binding domain (NCBI ptt file)||172, 200|
|CAC3298||bdhB||NADH-dependent butanol dehydrogenase B (BDH II) (NCBI ptt file)||172, 200|
|CAC3309||CAC3309||Predicted membrane protein (NCBI ptt file)||6, 19|
|CAC3353||CAC3353||Hypothetical protein (NCBI ptt file)||6, 327|
|CAC3576||CAC3576||Dioxygenase related to 2-nitropropane dioxygenase (NCBI ptt file)||6, 291|
|CAC3593||purA||Adenylosuccinate synthase (NCBI ptt file)||172, 254|
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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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.
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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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