Organism : Campylobacter jejuni | Module List :
Regulation information for Cj1300(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 Cj1300
Module neighborhood information for Cj1300
|Gene||Common Name||Description||Module membership|
|Cj0129c||Cj0129c||outer membrane protein (NCBI ptt file)||14, 133|
|Cj0149c||hom||homoserine dehydrogenase (NCBI ptt file)||62, 165|
|Cj0231c||nrdB||ribonucleoside-diphosphate reductase beta chain (NCBI ptt file)||133, 138|
|Cj0236c||Cj0236c||putative integral membrane protein (NCBI ptt file)||114, 133|
|Cj0268c||Cj0268c||putative transmembrane protein (NCBI ptt file)||111, 133|
|Cj0361||lspA||lipoprotein signal peptidase (NCBI ptt file)||52, 165|
|Cj0362||Cj0362||putative integral membrane protein (NCBI ptt file)||33, 165|
|Cj0392c||pyk||pyruvate kinase (NCBI ptt file)||91, 133|
|Cj0405||aroE||shikimate 5-dehydrogenase (NCBI ptt file)||60, 165|
|Cj0436||Cj0436||hypothetical protein Cj0436 (NCBI ptt file)||66, 133|
|Cj0496||Cj0496||hypothetical protein Cj0496 (NCBI ptt file)||35, 133|
|Cj0498||trpC||indole-3-glycerol phosphate synthase (NCBI ptt file)||100, 133|
|Cj0499||Cj0499||HIT-like protein (NCBI ptt file)||106, 133|
|Cj0615||pstA||putative phosphate transport system permease protein (NCBI ptt file)||132, 165|
|Cj0632||ilvC||ketol-acid reductoisomerase (NCBI ptt file)||102, 133|
|Cj0644||Cj0644||hypothetical protein Cj0644 (NCBI ptt file)||44, 165|
|Cj0683||Cj0683||putative periplasmic protein (NCBI ptt file)||88, 165|
|Cj0725c||mog||molybdopterin biosynthesis protein (NCBI ptt file)||143, 165|
|Cj0896c||pheT||phenylalanyl-tRNA synthetase beta chain (NCBI ptt file)||58, 133|
|Cj0931c||argH||argininosuccinate lyase (NCBI ptt file)||86, 133|
|Cj0932c||pckA||phosphoenolpyruvate carboxykinase (ATP) (NCBI ptt file)||102, 133|
|Cj0933c||pycB||putative pyruvate carboxylase B subunit (NCBI ptt file)||69, 133|
|Cj0936||atpE||ATP synthase F0 sector C subunit (NCBI ptt file)||111, 133|
|Cj0986c||Cj0986c||putative integral membrane protein (NCBI ptt file)||26, 133|
|Cj0987c||Cj0987c||putative integral membrane protein (NCBI ptt file)||32, 165|
|Cj0988c||Cj0988c||very hypothetical protein Cj0988c (NCBI ptt file)||155, 165|
|Cj0998c||Cj0998c||putative periplasmic protein (NCBI ptt file)||21, 133|
|Cj1020c||Cj1020c||putative cytochrome C (NCBI ptt file)||98, 133|
|Cj1073c||lon||ATP-dependent protease La (NCBI ptt file)||129, 165|
|Cj1093c||secD||protein-export membrane protein (NCBI ptt file)||14, 133|
|Cj1126c||wlaF||putative integral membrane protein (possible oligosaccharyl transferase) (NCBI ptt file)||117, 133|
|Cj1131c||galE||UDP-glucose 4-epimerase (NCBI ptt file)||111, 133|
|Cj1132c||Cj1132c||hypothetical protein Cj1132c (NCBI ptt file)||33, 165|
|Cj1164c||Cj1164c||hypothetical protein Cj1164c (NCBI ptt file)||98, 133|
|Cj1207c||Cj1207c||putative lipoprotein thiredoxin (NCBI ptt file)||51, 165|
|Cj1214c||Cj1214c||hypothetical protein Cj1214c (NCBI ptt file)||94, 165|
|Cj1294||Cj1294||putative aminotransferase (degT family) (NCBI ptt file)||120, 165|
|Cj1295||Cj1295||hypothetical protein Cj1295 (NCBI ptt file)||120, 165|
|Cj1296||Cj1296||hypothetical protein Cj1296 (NCBI ptt file)||152, 165|
|Cj1297||Cj1297||hypotehtical protein Cj1297 (NCBI ptt file)||120, 165|
|Cj1299||acpP2||putative acyl carrier protein (NCBI ptt file)||120, 165|
|Cj1300||Cj1300||hypothetical protein Cj1300 (NCBI ptt file)||133, 165|
|Cj1325||Cj1325||putative methyltransferase (NCBI)||117, 165|
|Cj1364c||fumC||fumarate hydratase (NCBI ptt file)||102, 133|
|Cj1409||acpS||putative holo-[acyl-carrier protein] synthase (NCBI ptt file)||136, 165|
|Cj1444c||kpsD||putative capsule polysaccharide export system periplasmic protein (NCBI ptt file)||88, 133|
|Cj1503c||putA||putative proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase (NCBI ptt file)||158, 165|
|Cj1518||moaE||possible molybdopterin converting factor, subunit 2 (NCBI ptt file)||133, 137|
|Cj1600||hisH||amidotransferase HisH (NCBI ptt file)||133, 141|
|Cj1626c||Cj1626c||putative periplasmic protein (NCBI ptt file)||86, 133|
|Cj1637c||Cj1637c||putative periplasmic protein (NCBI ptt file)||75, 165|
|Cj1675||fliQ||flagellar biosynthetic protein (NCBI ptt file)||26, 133|
|Cj1719c||leuA||2-isopropylmalate synthase (NCBI ptt file)||24, 165|
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.
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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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