Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC3478(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 CAC3478
|Gene||Common Name||Description||Module membership|
|CAC0168||CAC0168||T-RNA-processing ribonuclease BN (NCBI ptt file)||82, 207|
|CAC0204||srta||Sortase (surface protein transpeptidase), YHCS B.subtilis ortholog (NCBI ptt file)||115, 207|
|CAC0222||exoA||Exodeoxyribonuclease (exoA) (NCBI ptt file)||72, 207|
|CAC0250||CAC0250||Methyl-accepting chemotaxis protein (NCBI ptt file)||207, 258|
|CAC0314||CAC0314||Uncharacterized protein homolog YKRK B. subtilis (NCBI ptt file)||57, 207|
|CAC0345||CAC0345||Hypothetical protein (NCBI ptt file)||207, 361|
|CAC0357||CAC0357||Permease of the Na:galactoside symporter family (NCBI ptt file)||207, 361|
|CAC0358||CAC0358||Predicted xylanase/chitin deacetylase (NCBI ptt file)||165, 207|
|CAC0394||kdgA||Deoxyphosphogluconate aldolase (gene kdgA) (NCBI ptt file)||83, 326|
|CAC0431||CAC0431||Hypothetical protein, YitT family (NCBI ptt file)||169, 207|
|CAC0440||CAC0440||Homolog of osmotically induced OSMY protein of E.coli (NCBI ptt file)||62, 207|
|CAC0463||CAC0463||Serine protease Do (heat-shock protein) (NCBI ptt file)||207, 223|
|CAC0543||CAC0543||Methyl-accepting chemotaxis protein (NCBI ptt file)||207, 361|
|CAC0628||CAC0628||Putative Mn transporter, NRAMR family (NCBI ptt file)||191, 207|
|CAC0718||CAC0718||Ortholog ycnD B.subtilis, nitroreductase (NCBI ptt file)||83, 326|
|CAC0805||CAC0805||Methyl-accepting chemotaxis protein (NCBI ptt file)||24, 207|
|CAC0812||CAC0812||Pectate lyase related protein, secreted (NCBI ptt file)||108, 326|
|CAC0833||CAC0833||ABC-type multidrug transport system (daunorubicin resistance), ATPase component (NCBI ptt file)||115, 207|
|CAC0835||CAC0835||Predicted integral membrane protein (NCBI ptt file)||115, 207|
|CAC0886||CAC0886||Hypothetical protein (NCBI ptt file)||207, 270|
|CAC1018||CAC1018||Predicted membrane protein (NCBI ptt file)||287, 326|
|CAC1145||CAC1145||Hypothetical protein (NCBI ptt file)||326, 344|
|CAC1161||CAC1161||Predicted ATPase of HSP70 class (NCBI ptt file)||187, 326|
|CAC1198||recJ||Single-stranded-DNA-specific exonuclease (recJ) (NCBI ptt file)||187, 326|
|CAC1422||CAC1422||Uncharacterized CBS domain-containing protein, YUGS B.subtilis ortholog (NCBI ptt file)||207, 361|
|CAC1424||CAC1424||Zn-dependent hydrolase, glyoxylase II family (NCBI ptt file)||287, 326|
|CAC1548||trxB||Thioredoxin reductase (NCBI ptt file)||227, 326|
|CAC1657||CAC1657||Uncharacterized conserved protein, yisX B.subtilis ortholog (NCBI ptt file)||279, 326|
|CAC1658||CAC1658||Phospholipase D family protein (NCBI ptt file)||73, 326|
|CAC1670||CAC1670||Response regulator (CheY-like receiver domain and DNA-binding HTH domain) (NCBI ptt file)||185, 326|
|CAC1671||CAC1671||Predicted ATPase related to the helicase subunit of the Holliday junction resolvase (NCBI ptt file)||291, 326|
|CAC1672||CAC1672||Rad3-related DNA helicase (NCBI ptt file)||291, 326|
|CAC1970||CAC1970||Hypothetical protein (NCBI ptt file)||185, 326|
|CAC2057||CAC2057||D-alanyl-D-alanine carboxypeptidase (NCBI ptt file)||102, 207|
|CAC2178||CAC2178||Predicted CDP-4-keto-6-deoxy-D-glucose-3-dehydrase (NCBI ptt file)||326, 336|
|CAC2495||CAC2495||Predicted transcriptional regulator (NCBI ptt file)||258, 326|
|CAC2540||CAC2540||Co/Zn/Cd efflux system component (NCBI ptt file)||207, 301|
|CAC2545||CAC2545||Hypothetical protein (NCBI ptt file)||70, 326|
|CAC2684||CAC2684||Sugar kinase, ribokinase family (NCBI ptt file)||83, 326|
|CAC2814||CAC2814||Predicted membrane protein (NCBI ptt file)||153, 207|
|CAC2949||CAC2949||Predicted permease (NCBI ptt file)||207, 309|
|CAC3347||CAC3347||Amino acid transporter, permease (NCBI ptt file)||207, 276|
|CAC3468||uvrC||Excinuclease ABC, subunit C (uvrC) (NCBI ptt file)||207, 301|
|CAC3478||CAC3478||Predicted membrane protein (NCBI ptt file)||207, 326|
|CAC3516||CAC3516||Membrane-associated histidine kinase with HAMP domain (NCBI ptt file)||261, 326|
|CAC3517||CAC3517||Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file)||217, 326|
|CAC3519||CAC3519||Predicted membrane protein, possible permease (NCBI ptt file)||158, 207|
|CAC3520||CAC3520||ABC-type transport system, ATPase component (NCBI ptt file)||158, 207|
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
- 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
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