Organism : Campylobacter jejuni | Module List :
Regulation information for Cj1670c(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 Cj1670c
|Gene||Common Name||Description||Module membership|
|Cj0030||Cj0030||hypothetical protein Cj0030 (NCBI ptt file)||58, 128|
|Cj0031||Cj0031||putative type IIS restriction/modification enzyme (NCBI)||106, 141|
|Cj0082||cydB||cytochrome bd oxidase subunit II (NCBI ptt file)||44, 128|
|Cj0098||fmt||methionyl-tRNA formyltransferase (NCBI ptt file)||58, 128|
|Cj0100||Cj0100||parA family protein (NCBI ptt file)||65, 128|
|Cj0101||Cj0101||parB family protein (NCBI ptt file)||26, 128|
|Cj0124c||Cj0124c||putative membrane protein (NCBI ptt file)||23, 141|
|Cj0159c||Cj0159c||hypothetical protein Cj0159c (NCBI ptt file)||141, 149|
|Cj0189c||Cj0189c||hypothetical protein Cj0189c (NCBI ptt file)||76, 141|
|Cj0263||Cj0263||putative integral membrane protein (NCBI ptt file)||66, 128|
|Cj0320||fliH||putative flagellar assembly protein (NCBI ptt file)||99, 141|
|Cj0334||ahpC||alkyl hydroperoxide reductase (NCBI ptt file)||16, 128|
|Cj0504c||Cj0504c||hypothetical protein Cj0504c (NCBI ptt file)||48, 128|
|Cj0647||Cj0647||hypothetical protein Cj0647 (NCBI ptt file)||141, 151|
|Cj0701||Cj0701||putative protease (NCBI ptt file)||110, 141|
|Cj0702||purE||phosphoribosylaminoimidazole carboxylase catalytic subunit (NCBI ptt file)||83, 141|
|Cj0703||Cj0703||hypothetical protein Cj0703 (NCBI ptt file)||14, 141|
|Cj0707||kdtA||3-deoxy-D-manno-octulosonic-acid transferase (NCBI ptt file)||141, 149|
|Cj0708||Cj0708||putative ribosomal pseudouridine synthase (NCBI ptt file)||55, 141|
|Cj0770c||Cj0770c||putative periplasmic protein (NCBI ptt file)||94, 141|
|Cj0811||lpxK||putative tetraacyldisaccharide 4'-kinase (NCBI ptt file)||11, 141|
|Cj0825||Cj0825||putative processing peptidase (NCBI ptt file)||104, 141|
|Cj0957c||Cj0957c||hypothetical protein Cj0957c (NCBI ptt file)||141, 142|
|Cj0973||Cj0973||hypothetical protein Cj0973 (NCBI ptt file)||7, 141|
|Cj1013c||Cj1013c||putative membrane protein (NCBI ptt file)||128, 151|
|Cj1014c||livF||branched-chain amino-acid ABC transport system ATP-binding protein (NCBI ptt file)||128, 151|
|Cj1016c||livM||putative branched-chain amino-acid ABC transport system permease protein (NCBI ptt file)||104, 128|
|Cj1017c||livH||branched-chain amino-acid ABC transport system permease protein (NCBI ptt file)||128, 151|
|Cj1019c||livJ||branched-chain amino-acid ABC transport system periplasmic binding protein (NCBI ptt file)||61, 128|
|Cj1033||Cj1033||putative integral membrane component of efflux system (NCBI ptt file)||117, 128|
|Cj1130c||wlaB||ABC-type transport protein (NCBI ptt file)||62, 141|
|Cj1163c||Cj1163c||putative cation transport protein (NCBI ptt file)||51, 128|
|Cj1208||Cj1208||hypothetical protein Cj1208 (NCBI ptt file)||92, 128|
|Cj1246c||uvrC||excinuclease ABC subunit C (NCBI ptt file)||12, 141|
|Cj1282||mrdB||RodA protein homolog (NCBI ptt file)||26, 141|
|Cj1303||fabH2||putative 3-oxoacyl-[acyl-carrier-protein] synthase (NCBI ptt file)||106, 141|
|Cj1375||Cj1375||putative efflux protein (NCBI ptt file)||128, 148|
|Cj1385||katA||catalase (NCBI ptt file)||16, 128|
|Cj1415c||cysC||possible adenylylsulfate kinase (NCBI ptt file)||109, 141|
|Cj1440c||Cj1440c||putative sugar transferase (NCBI ptt file)||128, 141|
|Cj1479c||rpsI||30S ribosomal protein S9 (NCBI ptt file)||111, 128|
|Cj1533c||Cj1533c||putative helix-turn-helix containsing protein (NCBI ptt file)||109, 128|
|Cj1580c||Cj1580c||putative peptide ABC-transport system ATP-binding protein (NCBI ptt file)||56, 128|
|Cj1589||Cj1589||hypothetical protein Cj1589 (NCBI ptt file)||141, 146|
|Cj1600||hisH||amidotransferase HisH (NCBI ptt file)||133, 141|
|Cj1611||rpsT||30S ribosomal protein S20 (NCBI ptt file)||14, 141|
|Cj1643||Cj1643||putative periplasmic protein (NCBI ptt file)||62, 141|
|Cj1670c||Cj1670c||putative periplasmic protein (NCBI ptt file)||128, 141|
|Cj1688c||secY||preprotein translocase subunit (NCBI ptt file)||128, 151|
|Cj1689c||rplO||50S ribosomal protein L15 (NCBI ptt file)||128, 138|
|Cj1709c||Cj1709c||putative ribosomal pseudouridine synthase (NCBI ptt file)||128, 141|
|Cj1710c||Cj1710c||hypothetical protein Cj1710c (NCBI ptt file)||128, 151|
|Cj1711c||ksgA||putative dimethyladenosine transferase (16S rRNA dimethylase) (NCBI ptt file)||128, 151|
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.
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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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- 5. Module(s) that source gene and target genes belong to
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