Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC1334(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 CAC1334
Module neighborhood information for CAC1334
|Gene||Common Name||Description||Module membership|
|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|
|CAC0267||CAC0267||L-lactate dehydrogenase (NCBI ptt file)||33, 214|
|CAC0442||CAC0442||Permease, putative chloride channel (NCBI ptt file)||70, 214|
|CAC0546||CAC0546||Uncharacterized membrane protein, homolog of Methanobacterium (2621593) (NCBI ptt file)||95, 304|
|CAC0559||CAC0559||Transcriptional regulator, MarR/EmrR family (NCBI ptt file)||66, 214|
|CAC0587||CAC0587||Flavodoxin (NCBI ptt file)||214, 266|
|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|
|CAC0885||CAC0885||Ferredoxin 3 fused to uncharacterized domain, orthologous of AF0155 from Archaeoglobus fulgidus (NCBI ptt file)||214, 254|
|CAC0980||pflB||Pyruvate-formate lyase (NCBI ptt file)||214, 218|
|CAC0981||pflA||Pyruvate-formate-lyase-activating enzyme (NCBI ptt file)||214, 218|
|CAC1029||CAC1029||FeoA-like protein, involved in iron transport (NCBI ptt file)||83, 214|
|CAC1032||CAC1032||Predicted transcriptional regulator (NCBI ptt file)||83, 214|
|CAC1065||CAC1065||Uncharacterized protein, related stage III sporulation protein AH of Bacillus sp. (NCBI ptt file)||59, 304|
|CAC1274||rpsT||Ribosomal protein S20 (NCBI ptt file)||281, 304|
|CAC1334||CAC1334||Fe-S oxidoreductase of MoeA/NarA subfamily (NCBI ptt file)||214, 304|
|CAC1478||rpsD||Ribosomal protein S4 (NCBI ptt file)||83, 214|
|CAC1571||CAC1571||Glutathione peroxidase (NCBI ptt file)||70, 214|
|CAC1602||CAC1602||Predicted diverged CheY-domain (NCBI ptt file)||196, 214|
|CAC1655||purQ/purL||bifunctional enzyme phosphoribosylformylglycinamidine (FGAM) synthase (synthetase domain/glutamine amidotransferase domain) (NCBI ptt file)||214, 249|
|CAC1740||CAC1740||Uncharcaterized membrane protein, YLBJ B.subtilis homolog (NCBI ptt file)||59, 304|
|CAC2110||CAC2110||GAF domain-containing protein (NCBI ptt file)||233, 304|
|CAC2242||CAC2242||Predicted transcriptional regulator, arsE family (NCBI ptt file)||214, 247|
|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|
|CAC2820||CAC2820||Predicted permease (NCBI ptt file)||214, 319|
|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|
|CAC3552||CAC3552||Lactate dehydrogenase (NCBI ptt file)||214, 218|
|CAC3647||abrB||Transition state regulatory protein AbrB (NCBI ptt file)||281, 304|
|CAC3700||CAC3700||Hypothetical protein, CF-44 family (NCBI ptt file)||162, 304|
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.
You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".
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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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