Organism : Clostridium acetobutylicum | Module List :
Chromosome partitioning MinD-family ATPase, SOJ (NCBI ptt file)
Functional Annotations (3)
|ATPases involved in chromosome partitioning||cog/ cog|
|cobalamin biosynthetic process||go/ biological_process|
|cobyrinic acid a,c-diamide synthase activity||go/ molecular_function|
Regulation information for CAC3730(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 CAC3730
Module neighborhood information for CAC3730
|Gene||Common Name||Description||Module membership|
|CAC0125||dnaX||DNA-directed DNA polymerase, III chain (dnaX) (NCBI ptt file)||10, 356|
|CAC0150||CAC0150||Hypothetical protein (NCBI ptt file)||49, 286|
|CAC0151||CAC0151||Predicted SAM dependent methyltransferase (NCBI ptt file)||49, 157|
|CAC0220||CAC0220||Hypothetical protein (NCBI ptt file)||49, 261|
|CAC0247||CAC0247||Predicted permease (NCBI ptt file)||66, 356|
|CAC0271||CAC0271||Predicted esterase (NCBI ptt file)||49, 241|
|CAC0293||CAC0293||MccF-like protein (NCBI ptt file)||49, 191|
|CAC0605||CAC0605||Predicted phosphatase (NCBI ptt file)||287, 356|
|CAC0719||CAC0719||Epoxide hydrolase, similar to eukaryotic (NCBI ptt file)||150, 356|
|CAC0747||CAC0747||Secreted protein containing uncharacterized conserved protein of ErfK family (NCBI ptt file)||49, 185|
|CAC1002||CAC1002||Nicotinic acid phosphoribosyltransferase (NCBI ptt file)||49, 348|
|CAC1028||CAC1028||Hydrolase of alpha/beta superfamily, possible membrane associated lipase (NCBI ptt file)||276, 356|
|CAC1064||CAC1064||TPR-repeat-containing protein (NCBI ptt file)||49, 351|
|CAC1297||CAC1297||N-terminal fragment of elongation factor Ts (NCBI ptt file)||49, 109|
|CAC1330||CAC1330||Metal-dependent hydrolases of the beta-lactamase superfamily, possible sulfatase (NCBI ptt file)||287, 356|
|CAC1449||CAC1449||Hypothetical protein (NCBI ptt file)||239, 356|
|CAC1608||CAC1608||HIT family hydrolase (NCBI ptt file)||49, 265|
|CAC2362||thrS||Threonyl-tRNA synthetase (NCBI ptt file)||10, 356|
|CAC2473||CAC2473||Predicted transcriptional regulator (NCBI ptt file)||49, 87|
|CAC2520||CAC2520||Multimeric flavodoxin (WrbA) domain containing protein (NCBI ptt file)||49, 71|
|CAC2552||CAC2552||Predicted transcriptional regulator CRO family (NCBI ptt file)||196, 356|
|CAC2553||CAC2553||Uncharacterized mebrane protein, YOAS B.subtilis ortholog (NCBI ptt file)||196, 356|
|CAC2634||CAC2634||Ferric uptake regulator (FUR family), YGAG B.subtilis ortholog (NCBI ptt file)||49, 225|
|CAC2723||CAC2723||Deacethylase/dipeptidase/desuccinylase family of Zn-dependent hydrolases (NCBI ptt file)||49, 356|
|CAC2777||CAC2777||Glutaredoxin (NCBI ptt file)||49, 233|
|CAC2832||CAC2832||PLP-dependent aminotransferase (NCBI ptt file)||261, 356|
|CAC3165||CAC3165||Hypothetical protein (NCBI ptt file)||49, 325|
|CAC3284||CAC3284||Uncharacterized conserved protein, DegV family (NCBI ptt file)||49, 70|
|CAC3335||CAC3335||Short-chain alcohol dehydrogenase family enzyme (NCBI ptt file)||212, 356|
|CAC3336||CAC3336||Predicted cAMP-binding domain, regulatory protein, diverged (NCBI ptt file)||212, 356|
|CAC3457||CAC3457||Predicted membrane protein (NCBI ptt file)||287, 356|
|CAC3474||CAC3474||Predicted MDR-type permease (NCBI ptt file)||108, 356|
|CAC3508||CAC3508||Predicted aminopeptidase (NCBI ptt file)||240, 356|
|CAC3509||CAC3509||Transcriptional regulator, MerR family (duplicated domains) (NCBI ptt file)||287, 356|
|CAC3578||fabH||3-oxoacyl-[acyl-carrier-protein] synthase III (NCBI ptt file)||20, 356|
|CAC3579||CAC3579||Transcriptional regulator, MarR/EmrR family (NCBI ptt file)||20, 356|
|CAC3704||CAC3704||Hypothetical protein, CF-7 family (NCBI ptt file)||44, 356|
|CAC3712||CAC3712||Hypothetical protein (NCBI ptt file)||44, 356|
|CAC3729||spoOJ||Stage 0 sporulation J, ParB family of DNA-binding proteins (NCBI ptt file)||49, 224|
|CAC3730||soj||Chromosome partitioning MinD-family ATPase, SOJ (NCBI ptt file)||49, 356|
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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