Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC3394(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 CAC3394
Module neighborhood information for CAC3394
|Gene||Common Name||Description||Module membership|
|CAC0082||CAC0082||Predicted membrane protein (NCBI ptt file)||178, 292|
|CAC0115||CAC0115||Uncharacterized protein, Yje/RRF2 family (NCBI ptt file)||63, 232|
|CAC0217||pheA||Prephenate dehydrotase (pheA) (NCBI ptt file)||182, 292|
|CAC0322||CAC0322||Sensory protein, containing EAL-domain (NCBI ptt file)||232, 295|
|CAC0476||pepT||Peptidase T (aminotripeptidase), gene pepT (NCBI ptt file)||286, 292|
|CAC0493||CAC0493||Uncharcterized small conserved protein, YhhG family (NCBI ptt file)||64, 232|
|CAC0494||CAC0494||PemK family of DNA-binding proteins (NCBI ptt file)||32, 232|
|CAC0651||CAC0651||Hypothetical protein (NCBI ptt file)||292, 352|
|CAC0711||tpi||Triosephosphate isomerase (NCBI ptt file)||128, 292|
|CAC0712||pgm||2,3-bisphosphoglycerate-independent phosphoglycerate mutase gene (NCBI ptt file)||20, 292|
|CAC0944||tkt||Transketolase (NCBI ptt file)||84, 292|
|CAC1289||CAC1289||Uncharacterized conserved protein, YqeY B.subtilis ortholog (NCBI ptt file)||32, 232|
|CAC1356||thiH||Thiamine biosynthesis enzyme ThiH (NCBI ptt file)||196, 292|
|CAC1386||CAC1386||Zn-dependent hydrolases, glyoxylase family (NCBI ptt file)||182, 292|
|CAC1745||rpmF||Ribosomal protein L32 (NCBI ptt file)||32, 232|
|CAC1747||acpA||Acyl carrier protein, ACP (NCBI ptt file)||32, 232|
|CAC2286||CAC2286||Uncharacterized protein, similar to protein from Clostridium histolyticum (GI:3892648) (NCBI ptt file)||292, 352|
|CAC2484||CAC2484||Predicted membrane, YQJA B.subtilis ortholog (NCBI ptt file)||47, 292|
|CAC2711||bcd||Butyryl-CoA dehydrogenase (NCBI ptt file)||232, 255|
|CAC2712||crt||Crotonase (3-hydroxybutyryl-COA dehydratase) (NCBI ptt file)||61, 232|
|CAC2856||metK||S-adenosylmethionine synthetase (NCBI ptt file)||32, 232|
|CAC3023||CAC3023||Hypothetical protein (NCBI ptt file)||268, 292|
|CAC3109||infA||Translation initiation factor IF-1 (NCBI ptt file)||255, 292|
|CAC3113||seqY||Preprotein translocase subunit SecY (NCBI ptt file)||292, 304|
|CAC3135||CAC3135||Uncharacterized C4-type Zn-finger containing protein (NCBI ptt file)||232, 237|
|CAC3145||rplL||Ribosomal protein L7/L12 (NCBI ptt file)||61, 232|
|CAC3147||rplA||Ribosomal protein L1 (NCBI ptt file)||61, 232|
|CAC3150||secE||Preprotein translocase subunit SecE (NCBI ptt file)||116, 232|
|CAC3175||CAC3175||Hypothetical protein (NCBI ptt file)||73, 292|
|CAC3201||CAC3201||Formate--tetrahydrofolate ligase (NCBI ptt file)||201, 292|
|CAC3202||ftsH||ATP-dependent Zn protease, FTSH (NCBI ptt file)||273, 292|
|CAC3224||purR||PUR operon repressor, Adenine/guanine phosphoribosyltransferase family (NCBI ptt file)||232, 292|
|CAC3225||murC||UDP-N-acetylmuramate-alanine ligase (NCBI ptt file)||292, 359|
|CAC3252||proC||Pyrroline-5-carboxylate reductase (NCBI ptt file)||85, 232|
|CAC3260||asnS||Aspartyl/asparaginyl-tRNA synthetase (NCBI ptt file)||82, 292|
|CAC3376||CAC3376||Possible pectin degradation protein (sugar phosphate isomerase family) (NCBI ptt file)||113, 292|
|CAC3394||CAC3394||Uncharacterized conserved protein, YGIN family (NCBI ptt file)||232, 292|
|CAC3595||CAC3595||Uncharacterized FAD-dependent dehydrogenase (NCBI ptt file)||182, 292|
|CAC3695||CAC3695||Possible transcriptional regulator, containing DNA-binding domain of xre family (NCBI ptt file)||113, 292|
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".
For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.
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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