Organism : Clostridium acetobutylicum | Module List :
Transition state regulatory protein AbrB (NCBI ptt file)
Functional Annotations (2)
|Regulators of stationary/sporulation gene expression||cog/ cog|
Regulation information for CAC3647(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 CAC3647
|Regulators of stationary/sporulation gene expression||cog/ cog|
Module neighborhood information for CAC3647
|Gene||Common Name||Description||Module membership|
|CAC0126||CAC0126||Uncharacterized conserved protein, YbaB family (NCBI ptt file)||10, 281|
|CAC0127||recR||Recombination protein (recR) (NCBI ptt file)||32, 281|
|CAC0128||CAC0128||Hypothetical protein (NCBI ptt file)||281, 304|
|CAC0129||bofA||BofA B.subtilis ortholog, SigmaK-factor processing regulatory protein (NCBI ptt file)||77, 304|
|CAC0228||CAC0228||Hypothetical protein (NCBI ptt file)||304, 322|
|CAC0528||CAC0528||ABC transporter, ATPase component (two ATPase domains) (NCBI ptt file)||249, 281|
|CAC0546||CAC0546||Uncharacterized membrane protein, homolog of Methanobacterium (2621593) (NCBI ptt file)||95, 304|
|CAC0716||smpB||TmRNA-binding protein SmpB (NCBI ptt file)||53, 304|
|CAC0730||CAC0730||Predicted permease (NCBI ptt file)||146, 304|
|CAC0771||CAC0771||Cobalamin biosynthesis protein CbiM (NCBI ptt file)||262, 304|
|CAC0868||CAC0868||Predicted membrane protein (NCBI ptt file)||118, 304|
|CAC0965||CAC0965||1-acyl-sn-glycerol-3-phosphate acyltransferase (NCBI ptt file)||58, 281|
|CAC0992||CAC0992||Hypothetical protein (NCBI ptt file)||73, 281|
|CAC1065||CAC1065||Uncharacterized protein, related stage III sporulation protein AH of Bacillus sp. (NCBI ptt file)||59, 304|
|CAC1239||CAC1239||Predicted membrane protein (NCBI ptt file)||172, 281|
|CAC1240||maf||Maf protein ortholog, putative inhibitor of septum formation (NCBI ptt file)||229, 281|
|CAC1251||rodA||Cell division protein, rodA/ftsW/spoVE family (NCBI ptt file)||76, 281|
|CAC1274||rpsT||Ribosomal protein S20 (NCBI ptt file)||281, 304|
|CAC1334||CAC1334||Fe-S oxidoreductase of MoeA/NarA subfamily (NCBI ptt file)||214, 304|
|CAC1654||CAC1654||Zn-dependent metalloprotease, insulinase family (NCBI ptt file)||105, 281|
|CAC1719||rpoZ||RNA polymerase-associated protein RpoZ, omega subunit (YLOH B.subtilis ortholog) (NCBI ptt file)||172, 281|
|CAC1740||CAC1740||Uncharcaterized membrane protein, YLBJ B.subtilis homolog (NCBI ptt file)||59, 304|
|CAC1762||rnh||Ribonuclease HII (NCBI ptt file)||116, 281|
|CAC1785||topA||Topoisomerase I (NCBI ptt file)||79, 281|
|CAC2030||CAC2030||Hypothetical protein (NCBI ptt file)||270, 281|
|CAC2094||efp||Translation elongation factor P (NCBI ptt file)||152, 281|
|CAC2110||CAC2110||GAF domain-containing protein (NCBI ptt file)||233, 304|
|CAC2183||CAC2183||Uncharacterized protein, posible homoloh of YJFB B. subtilis (NCBI ptt file)||281, 286|
|CAC2228||CAC2228||Hypothetical protein (NCBI ptt file)||76, 281|
|CAC2299||hflX||Predicted GTPase, HflX (NCBI ptt file)||35, 304|
|CAC2476||CAC2476||Uncharacterized protein, homolog of Spirochaeta aurantia (gi:152901) (NCBI ptt file)||38, 304|
|CAC2477||CAC2477||Hypothetical protein (NCBI ptt file)||38, 304|
|CAC2641||tig||FKBP-type peptidyl-prolyl cis-transisomerase (trigger factor) (NCBI ptt file)||304, 329|
|CAC2665||CAC2665||Xanthosine triphosphate pyrophosphatase, HAM1-like protein (NCBI ptt file)||64, 281|
|CAC2671||CAC2671||Glu-tRNAGln amidotransferase subunit C (NCBI ptt file)||79, 281|
|CAC2713||CAC2713||AT-rich DNA-binding protein (NCBI ptt file)||76, 281|
|CAC2769||ppiB||Peptidyl-prolyl cis-transisomerase, cyclophilin family (NCBI ptt file)||254, 281|
|CAC2864||atpC||FoF1-type ATP synthase epsilon subunit (NCBI ptt file)||304, 335|
|CAC2865||atpD||FoF1-type ATP synthase beta subunit (NCBI ptt file)||59, 304|
|CAC2870||atpE||FoF1-type ATP synthase C subunit (NCBI ptt file)||59, 304|
|CAC2888||rpmE||50S ribosomal protein L31 (NCBI ptt file)||38, 304|
|CAC3038||ileS||Isoleucyl-tRNA synthetase (NCBI ptt file)||146, 304|
|CAC3104||rpoA||DNA-dependent RNA polymerase alpha subunit (NCBI ptt file)||8, 304|
|CAC3113||seqY||Preprotein translocase subunit SecY (NCBI ptt file)||292, 304|
|CAC3122||rplX||Ribosomal protein L24 (NCBI ptt file)||255, 304|
|CAC3210||CAC3210||Predicted RNA-binding protein, YABO B.subtilis ortholog (NCBI ptt file)||215, 281|
|CAC3287||CAC3287||Predicted membrane protein (NCBI ptt file)||105, 281|
|CAC3647||abrB||Transition state regulatory protein AbrB (NCBI ptt file)||281, 304|
|CAC3700||CAC3700||Hypothetical protein, CF-44 family (NCBI ptt file)||162, 304|
|CAC3739||rpmH||L34 (NCBI ptt file)||201, 281|
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.
Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
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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.
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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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