Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC0492(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 CAC0492
Module neighborhood information for CAC0492
|Gene||Common Name||Description||Module membership|
|CAC0175||CAC0175||Predicted sugar phosphate isomerase, homolog of eucaryotic glucokinase regulator (NCBI ptt file)||15, 318|
|CAC0176||appA||Oligopeptide-binding protein, periplasmic component (NCBI ptt file)||22, 318|
|CAC0193||CAC0193||Uncharacterized conserved membrane protein, affecting LPS biosynthesis (NCBI ptt file)||7, 174|
|CAC0194||CAC0194||Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file)||7, 174|
|CAC0444||napA||Na/H antiporter (napA) (NCBI ptt file)||62, 174|
|CAC0467||CAC0467||Uncharacterized membrane protein, homolog of YDAH B.subtilis (NCBI ptt file)||78, 174|
|CAC0492||CAC0492||Alanine racemase (NCBI ptt file)||174, 318|
|CAC0655||CAC0655||Hypothetical protein, CF-26 family (NCBI ptt file)||278, 318|
|CAC0668||CAC0668||Predicted membrane protein (NCBI ptt file)||174, 305|
|CAC0678||CAC0678||CBS domains (NCBI ptt file)||160, 174|
|CAC0704||CAC0704||Sugar ABC transporter, permease protein (NCBI ptt file)||95, 174|
|CAC0840||potA||Spermidine/putrescine ABC transporter, ATP-binding component (NCBI ptt file)||153, 174|
|CAC1099||CAC1099||P-loop kinase (uridine kinase family) (NCBI ptt file)||274, 318|
|CAC1468||CAC1468||Predicted acetyltransferase (NCBI ptt file)||174, 315|
|CAC1588||CAC1588||Malolactic regulator, LysR family (NCBI ptt file)||174, 366|
|CAC1695||sigE||DNA-dependent RNA polymerase sigma subunit (NCBI ptt file)||199, 318|
|CAC1696||sigG||Specialized DNA-dependent RNA polymerase sigma subunit (NCBI ptt file)||174, 235|
|CAC1968||CAC1968||Pectate lyase related enzyme (NCBI ptt file)||174, 314|
|CAC1983||CAC1983||Hypothetical protein (NCBI ptt file)||200, 318|
|CAC2433||CAC2433||HtrA-like serine protease (with PDZ domain) (NCBI ptt file)||200, 318|
|CAC2438||CAC2438||Predicted phosphatase (NCBI ptt file)||174, 300|
|CAC2575||rubY||Rubrerythrin (NCBI ptt file)||184, 318|
|CAC2875||tagO||Undecaprenyl-phosphate (NCBI ptt file)||174, 235|
|CAC3032||CAC3032||Galactose mutarotase related enzyme (NCBI ptt file)||174, 315|
|CAC3157||trpA||Tryptophan synthase alpha chain (NCBI ptt file)||12, 318|
|CAC3158||trpB||Tryptophan synthase beta chain (NCBI ptt file)||12, 318|
|CAC3159||trpF||Phosphoribosylanthranilate isomerase (NCBI ptt file)||12, 318|
|CAC3160||trpC||Indole-3-glycerol phosphate synthase (NCBI ptt file)||12, 318|
|CAC3161||trpD||Anthranilate phosphoribosyltransferase (NCBI ptt file)||12, 318|
|CAC3162||pabA||Para-aminobenzoate synthase component II (NCBI ptt file)||12, 318|
|CAC3163||parB||Para-aminobenzoate synthase component I (NCBI ptt file)||12, 318|
|CAC3220||CAC3220||Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file)||44, 174|
|CAC3230||CAC3230||Hydrogenase subunit (ferredoxin) (NCBI ptt file)||174, 330|
|CAC3357||CAC3357||Hypothetical protein (NCBI ptt file)||118, 174|
|CAC3590||CAC3590||Predicted flavoprotein, YhiN family (NCBI ptt file)||174, 301|
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)
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