Organism : Campylobacter jejuni | Module List :
Regulation information for Cj0864(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 Cj0864
|Gene||Common Name||Description||Module membership|
|Cj0007||gltB||glutamate synthase (NADPH) large subunit (NCBI ptt file)||28, 119|
|Cj0008||Cj0008||hypothetical protein Cj0008 (NCBI ptt file)||86, 119|
|Cj0016||Cj0016||putative transcriptional regulatory protein (NCBI ptt file)||10, 158|
|Cj0073c||Cj0073c||hypothetical protein Cj0073c (NCBI ptt file)||119, 126|
|Cj0074c||Cj0074c||putative iron-sulfur protein (NCBI ptt file)||119, 126|
|Cj0075c||Cj0075c||putative oxidoreductase iron-sulfur subunit (NCBI ptt file)||119, 126|
|Cj0076c||lctP||L-lactate permease (NCBI ptt file)||119, 126|
|Cj0138||Cj0138||hypothetical protein Cj0138 (NCBI ptt file)||11, 158|
|Cj0260c||Cj0260c||small hydrophobic protein (NCBI ptt file)||39, 158|
|Cj0272||Cj0272||hypothetical protein Cj0272 (NCBI ptt file)||39, 158|
|Cj0310c||Cj0310c||putative efflux protein (NCBI ptt file)||95, 158|
|Cj0366c||Cj0366c||transmembrane efflux protein (NCBI ptt file)||83, 158|
|Cj0448c||Cj0448c||putative MCP-type signal transduction protein (NCBI ptt file)||35, 119|
|Cj0449c||Cj0449c||hypothetical protein Cj0449c (NCBI ptt file)||87, 119|
|Cj0458c||Cj0458c||hypothetical protein Cj0458c (NCBI ptt file)||61, 158|
|Cj0483||uxaA'||putative altronate hydrolase C-terminus (RefSeq)||28, 119|
|Cj0484||Cj0484||transmembrane transport protein (NCBI ptt file)||28, 119|
|Cj0533||sucC||succinyl-coA synthetase beta chain (NCBI ptt file)||119, 126|
|Cj0552||Cj0552||hydrophobic protein (NCBI ptt file)||119, 120|
|Cj0553||Cj0553||putative integral membrane protein (NCBI ptt file)||119, 120|
|Cj0554||Cj0554||hypothetical protein Cj0554 (NCBI ptt file)||119, 155|
|Cj0555||Cj0555||putative integral membrane protein (NCBI ptt file)||132, 158|
|Cj0604||Cj0604||hypothetical protein Cj0604 (NCBI ptt file)||119, 127|
|Cj0607||Cj0607||ABC-type transmembrane transport protein (NCBI ptt file)||145, 158|
|Cj0620||Cj0620||hypothetical protein Cj0620 (NCBI ptt file)||76, 158|
|Cj0668||Cj0668||putative ATP /GTP-binding protein (NCBI ptt file)||158, 160|
|Cj0688||pta||putative phosphate acetyltransferase (NCBI ptt file)||86, 119|
|Cj0689||ackA||acetate kinase (NCBI ptt file)||86, 119|
|Cj0704||glyQ||glycyl-tRNA synthetase alpha chain (NCBI ptt file)||56, 158|
|Cj0824||uppS||putative undecaprenyl diphosphate synthase (NCBI ptt file)||104, 158|
|Cj0835c||acnB||aconitate hydratase (NCBI ptt file)||119, 126|
|Cj0864||Cj0864||putative periplasmic protein (NCBI ptt file)||119, 158|
|Cj0884||rpsO||30S ribosomal protein S15 (NCBI ptt file)||26, 158|
|Cj0893c||rpsA||30S ribosomal protein S1 (NCBI ptt file)||91, 119|
|Cj0917c||cstA||carbon starvation protein A homolog (NCBI ptt file)||56, 158|
|Cj1173||Cj1173||putative efflux protein (NCBI ptt file)||123, 158|
|Cj1174||Cj1174||putative efflux protein (NCBI ptt file)||109, 158|
|Cj1257c||Cj1257c||putative efflux pump (NCBI ptt file)||145, 158|
|Cj1374c||Cj1374c||hypothetical protein Cj1374c (NCBI ptt file)||148, 158|
|Cj1430c||Cj1430c||putative nucleotide-sugar epimerase/dehydratase (NCBI ptt file)||24, 158|
|Cj1454c||Cj1454c||hypothetical protein Cj1454c (NCBI ptt file)||125, 158|
|Cj1503c||putA||putative proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase (NCBI ptt file)||158, 165|
|Cj1532||Cj1532||possible periplasmic protein (NCBI ptt file)||81, 158|
|Cj1541||Cj1541||hypothetical protein Cj1541 (NCBI ptt file)||119, 120|
|Cj1546||Cj1546||hypothetical protein Cj1546 (NCBI ptt file)||56, 158|
|Cj1584c||Cj1584c||putative peptide ABC-transport system periplasmic peptide-binding protein (NCBI ptt file)||56, 158|
|Cj1607||Cj1607||hypothetical protein Cj1607 (NCBI ptt file)||54, 158|
|Cj1610||pgpA||putative phosphatidylglycerophosphatase (NCBI ptt file)||11, 158|
|Cj1633||Cj1633||hypothetical protein Cj1633 (NCBI ptt file)||51, 158|
|Cj1654c||nhaA2||Na(+)/H(+) antiporter (NCBI ptt file)||132, 158|
|Cj1682c||gltA||citrate synthase (NCBI ptt file)||87, 119|
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.
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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.
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