Organism : Campylobacter jejuni | Module List :
Regulation information for Cj1178c(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 Cj1178c
|Gene||Common Name||Description||Module membership|
|Cj0085c||Cj0085c||putative amino acid recemase (NCBI ptt file)||77, 157|
|Cj0282c||serB||putative phosphoserine phosphatase (NCBI ptt file)||77, 122|
|Cj0298c||panB||3-methyl-2-oxobutanoate hydroxymethyltransferase (NCBI ptt file)||98, 142|
|Cj0337c||motA||putative flagellar motor proton channel (NCBI ptt file)||74, 142|
|Cj0350||Cj0350||hypothetical protein Cj0350 (NCBI ptt file)||91, 142|
|Cj0377||Cj0377||probable AAA family ATPase (NCBI ptt file)||13, 77|
|Cj0378c||Cj0378c||putative integral membrane protein (NCBI ptt file)||77, 168|
|Cj0383c||ribH||6,7-dimethyl-8-ribityllumazine synthase (NCBI ptt file)||82, 142|
|Cj0384c||kdsA||2-dehydro-3-deoxyphosphooctonate aldolase (NCBI ptt file)||142, 170|
|Cj0393c||Cj0393c||putative oxidoreductase (NCBI ptt file)||87, 142|
|Cj0426||Cj0426||ABC transporter ATP-binding protein (NCBI ptt file)||91, 142|
|Cj0427||Cj0427||hypothetical protein Cj0427 (NCBI ptt file)||91, 142|
|Cj0433c||mraY||phospho-N-acetylmuramoyl-pentapeptide- transferase (NCBI ptt file)||77, 125|
|Cj0513||Cj0513||hypothetical protein Cj0513 (NCBI ptt file)||116, 142|
|Cj0527c||flgC||flagellar basal-body rod protein (NCBI ptt file)||142, 170|
|Cj0529c||Cj0529c||hypothetical protein Cj0529c (NCBI ptt file)||77, 122|
|Cj0612c||cft||ferritin (NCBI ptt file)||142, 170|
|Cj0618||Cj0618||hypothetical protein Cj0618 (617 family) (NCBI ptt file)||77, 129|
|Cj0922c||pebC||ABC-type amino-acid transporter ATP-binding protein (NCBI ptt file)||91, 142|
|Cj0941c||Cj0941c||putative integral membrane protein (NCBI ptt file)||77, 168|
|Cj0943||Cj0943||putative periplasmic protein (NCBI ptt file)||17, 77|
|Cj0954c||Cj0954c||putative dnaJ-like protein (NCBI ptt file)||26, 77|
|Cj0957c||Cj0957c||hypothetical protein Cj0957c (NCBI ptt file)||141, 142|
|Cj1029c||mapA||putative lipoprotein (NCBI ptt file)||20, 142|
|Cj1075||Cj1075||hypothetical protein Cj1075 (NCBI ptt file)||137, 142|
|Cj1107||Cj1107||hypothetical protein Cj1107 (NCBI ptt file)||77, 114|
|Cj1118c||cheY||chemotaxis regulatory protein (NCBI ptt file)||43, 142|
|Cj1176c||Cj1176c||hypothetical protein Cj1176c (NCBI ptt file)||137, 142|
|Cj1178c||Cj1178c||highly acidic protein (NCBI ptt file)||77, 142|
|Cj1183c||cfa||putative cyclopropane-fatty-acyl-phospholipid synthase (NCBI ptt file)||77, 136|
|Cj1211||Cj1211||putative integral membrane protein (NCBI ptt file)||67, 77|
|Cj1212c||rbn||putative ribonuclease BN (NCBI ptt file)||77, 161|
|Cj1273c||rpoZ||putative DNA-directed RNA polymerase omega chain (NCBI ptt file)||142, 170|
|Cj1274c||pyrH||uridylate kinase (NCBI ptt file)||142, 170|
|Cj1304||acpP3||putative acyl carrier protein (NCBI ptt file)||77, 89|
|Cj1310c||Cj1310c||hypothetical protein Cj1310c (617 family) (NCBI ptt file)||51, 77|
|Cj1332||ptmA||putative oxidoreductase (flagellin modification) (NCBI ptt file)||63, 77|
|Cj1403c||gapA||glyceraldehyde 3-phosphate dehydrogenase (NCBI ptt file)||137, 142|
|Cj1408||fliL||possible flagellar protein (NCBI ptt file)||91, 142|
|Cj1419c||Cj1419c||possible methyltransferase (NCBI ptt file)||91, 142|
|Cj1445c||kpsE||putative capsule polysaccharide export system inner membrane protein (NCBI ptt file)||77, 84|
|Cj1478c||cadF||outer membrane fibronectin-binding protein (NCBI ptt file)||82, 142|
|Cj1537c||acs||acetyl-coenzyme A synthetase (NCBI ptt file)||77, 157|
|Cj1588c||Cj1588c||putative transmembrane transport protein (NCBI ptt file)||77, 103|
|Cj1612||prfA||peptide chain release factor 1 (NCBI ptt file)||77, 131|
|Cjp08||tRNA-Gly||tRNA-Gly (NCBI)||77, 85|
|Cjt01||tRNA-Leu||tRNA-Leu (NCBI)||77, 110|
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
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