Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC3039(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|
Module neighborhood information for CAC3039
|Gene||Common Name||Description||Module membership|
|CAC0018||CAC0018||Putative NADPH-quinone reductase, YabF family (NCBI ptt file)||256, 327|
|CAC0166||CAC0166||Uncharacterized conserved protein (NCBI ptt file)||177, 245|
|CAC0365||CAC0365||Phosphoglycerate dehydrogenase (NCBI ptt file)||256, 316|
|CAC0367||rocB||Arginine degradation protein (gene rocB) (NCBI ptt file)||256, 271|
|CAC0376||CAC0376||N-dimethylarginine dimethylaminohydrolase (similar to ykgA B.subtilis) (NCBI ptt file)||111, 256|
|CAC0377||CAC0377||Amino acid (glutamine) ABC transporter, permease component (NCBI ptt file)||172, 256|
|CAC0397||CAC0397||Predicted sugar phosphate aminotransferase involved in capsule formation (NCBI ptt file)||136, 245|
|CAC0574||CAC0574||Pectate lyase H (FS) (NCBI ptt file)||123, 256|
|CAC0643||CAC0643||Putative spore germination protein (NCBI ptt file)||136, 245|
|CAC0998||CAC0998||Homoserine dehydrogenase (NCBI ptt file)||234, 256|
|CAC0999||thrC||Threonine synthase (NCBI ptt file)||234, 256|
|CAC1000||CAC1000||Uncharacterized protein, homolog of yhfF B.subtilis (NCBI ptt file)||256, 327|
|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|
|CAC1268||comEA||Competence ComEA protein (NCBI ptt file)||243, 245|
|CAC1300||sigA||RNA polymerase sigma factor RPOD (NCBI ptt file)||159, 256|
|CAC1352||CAC1352||Membrane associated chemotaxis sensory transducer protein (MSP domain and HAMP domain) (NCBI ptt file)||137, 256|
|CAC1421||CAC1421||Pyruvate-formate lyase-activating enzyme (NCBI ptt file)||188, 245|
|CAC1427||gabT||4-aminobutyrate aminotransferase (PLP-dependent) (NCBI ptt file)||111, 256|
|CAC1505||CAC1505||Hypothetical protein (NCBI ptt file)||245, 257|
|CAC1616||CAC1616||Hypothetical protein (NCBI ptt file)||188, 245|
|CAC1705||CAC1705||Periplasmic phosphate-binding protein (NCBI ptt file)||245, 337|
|CAC1706||CAC1706||Phosphate permease (NCBI ptt file)||118, 245|
|CAC1707||CAC1707||Permease component of ATP-dependent phosphate uptake system (NCBI ptt file)||118, 245|
|CAC1708||CAC1708||ATPase component of ABC-type phosphate transport system (NCBI ptt file)||103, 245|
|CAC1765||CAC1765||ATPase, possible competence protein ComM (NCBI ptt file)||39, 245|
|CAC2105||CAC2105||General secretion pathway protein E, ATPase (NCBI ptt file)||256, 320|
|CAC2351||CAC2351||Glycosyltransferase (NCBI ptt file)||100, 256|
|CAC2368||CAC2368||Hypothetical protein (NCBI ptt file)||254, 256|
|CAC2815||CAC2815||Hypothetical protein (NCBI ptt file)||101, 245|
|CAC2882||CAC2882||Predicted translation factor (SUA5) (NCBI ptt file)||79, 256|
|CAC2885||CAC2885||S-adenosylmethionine-dependent methyltransferase, HEMK ortholog (NCBI ptt file)||229, 256|
|CAC2886||CAC2886||Uncharacterized conserved protein, predicted metal-dependent enzyme, YQHQ B.subtilis ortholog (NCBI ptt file)||79, 256|
|CAC2989||CAC2989||PHP superfamily hydrolase, YABD ortholog (NCBI ptt file)||254, 256|
|CAC3039||CAC3039||Hypothetical secreted protein (NCBI ptt file)||245, 256|
|CAC3096||thiK||Hydroxyethylthiazole kinase ThiM/ThiK (FS!) (NCBI ptt file)||256, 316|
|CAC3166||CAC3166||Predicted DNA-binding protein (NCBI ptt file)||30, 245|
|CAC3199||CAC3199||NifR3 family enzyme (NCBI ptt file)||79, 256|
|CAC3421||CAC3421||Acyl carrier protein phosphodiesterase (NCBI ptt file)||177, 245|
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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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
- 3. Target genes (other module members)
- 4. Interactions between source and target genes for a particular module
- 5. Module(s) that source gene and target genes belong to
- 6. Visualisation legend