Organism : Campylobacter jejuni
| Module List :
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Cj1218c ribA
putative riboflavin synthase alpha chain (NCBI ptt file)
Functional Annotations (6)
Function | System |
---|---|
Riboflavin synthase alpha chain | cog/ cog |
riboflavin synthase activity | go/ molecular_function |
riboflavin synthase complex | go/ cellular_component |
Riboflavin metabolism | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
ribE | tigr/ tigrfam |
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Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
Motif Id | e-value | Consensus | Motif Logo |
---|---|---|---|
7602 | 1.70e+02 | ccAAAagCtct |
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7603 | 3.70e+03 | GCCCaGc |
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7702 | 3.50e+01 | tatTaAgt.aaatTttgaTA.aAT |
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7703 | 7.30e+03 | AaCaTcAagggtatttGcaatAG |
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Functional Enrichment for Cj1218c
Function | System |
---|---|
Riboflavin synthase alpha chain | cog/ cog |
riboflavin synthase activity | go/ molecular_function |
riboflavin synthase complex | go/ cellular_component |
Riboflavin metabolism | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
ribE | tigr/ tigrfam |
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Module neighborhood information for Cj1218c
Gene | Common Name | Description | Module membership |
---|---|---|---|
Cj0028 | recJ | putative single-stranded-DNA-specific exonuclease (NCBI ptt file) | 24, 160 |
Cj0055c | Cj0055c | hypothetical protein Cj0055c (NCBI ptt file) | 110, 149 |
Cj0106 | atpG | ATP synthase F1 sector gamma subunit (NCBI ptt file) | 60, 110 |
Cj0194 | folE | GTP cyclohydrolase I (NCBI ptt file) | 95, 160 |
Cj0205 | bacA | putative undecaprenol kinase (bacitracin resistance protein) (NCBI ptt file) | 98, 110 |
Cj0265c | Cj0265c | putative cytochrome C-type haem-binding periplasmic protein (NCBI ptt file) | 82, 160 |
Cj0270 | Cj0270 | possible isomserase (NCBI ptt file) | 130, 160 |
Cj0287c | greA | transcription elongation factor (NCBI ptt file) | 95, 160 |
Cj0371 | Cj0371 | putative flagellar motility protein (NCBI ptt file) | 13, 110 |
Cj0398 | gatC | putative Glu-tRNAGln amidotransferase subunit C (NCBI ptt file) | 132, 160 |
Cj0434 | pgm | phosphoglycerate mutase (NCBI ptt file) | 24, 160 |
Cj0532 | mdh | malate dehydrogenase (NCBI ptt file) | 11, 110 |
Cj0549 | fliS | flagellar protein (NCBI ptt file) | 130, 160 |
Cj0558c | proA | gamma-glutamyl phosphate reductase (NCBI ptt file) | 110, 116 |
Cj0572 | ribA | GTP cyclohydrolase II / 3,4-dihydroxy-2-butanone 4-phosphate synthase (NCBI ptt file) | 110, 130 |
Cj0573 | Cj0573 | hypothetical protein Cj0573 (NCBI ptt file) | 110, 130 |
Cj0574 | ilvI | acetolactate synthase large subunit (NCBI ptt file) | 11, 110 |
Cj0575 | ilvH | acetolactate synthase small subunit (NCBI ptt file) | 13, 110 |
Cj0576 | lpxD | UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (NCBI ptt file) | 37, 110 |
Cj0628 | Cj0628 | putative lipoprotein (NCBI) | 110, 130 |
Cj0663c | hslV | putative heat shock protein (NCBI ptt file) | 137, 160 |
Cj0668 | Cj0668 | putative ATP /GTP-binding protein (NCBI ptt file) | 158, 160 |
Cj0701 | Cj0701 | putative protease (NCBI ptt file) | 110, 141 |
Cj0713 | trmD | tRNA (guanine-N1)-methyltransferase (NCBI ptt file) | 132, 160 |
Cj0802 | cysS | cysteinyl-tRNA synthetase (NCBI ptt file) | 69, 110 |
Cj0805 | Cj0805 | putative zinc protease (NCBI ptt file) | 110, 122 |
Cj0820c | fliP | flagellar biosynthesis protein (NCBI ptt file) | 104, 160 |
Cj0821 | glmU | UDP-N-acetylglucosamine pyrophosphorylase (NCBI ptt file) | 104, 110 |
Cj0899c | thiJ | 4-methyl-5(beta-hydroxyethyl)-thiazole monophosphate synthesis protein (NCBI ptt file) | 110, 137 |
Cj0923c | cheR | putative MCP protein methyltransferase (NCBI ptt file) | 60, 110 |
Cj0965c | Cj0965c | hypothetical protein Cj0965c (NCBI ptt file) | 139, 160 |
Cj1024c | Cj1024c | signal-transduction regulatory protein (NCBI ptt file) | 132, 160 |
Cj1030c | lepA | lepA GTP-binding protein homolog (NCBI ptt file) | 63, 160 |
Cj1060c | Cj1060c | small hydrophobic protein (NCBI ptt file) | 110, 160 |
Cj1117c | prmA | possible ribosomal protein methyltransferase (NCBI ptt file) | 60, 160 |
Cj1181c | tsf | elongation factor TS (NCBI ptt file) | 30, 160 |
Cj1197c | gatB | Glu-tRNAGln amidotransferase subunit B (NCBI ptt file) | 64, 110 |
Cj1204c | atpB | ATP synthase F0 sector A subunit (NCBI ptt file) | 160, 166 |
Cj1218c | ribA | putative riboflavin synthase alpha chain (NCBI ptt file) | 110, 160 |
Cj1234 | glyS | glycyl-tRNA synthetase beta chain (NCBI ptt file) | 132, 160 |
Cj1242 | Cj1242 | hypothetical protein Cj1242 (NCBI ptt file) | 130, 160 |
Cj1288c | gltX2 | glutamyl-tRNA synthetase (NCBI ptt file) | 34, 160 |
Cj1401c | tpiA | putative triosephosphate isomerase (NCBI ptt file) | 110, 137 |
Cj1402c | pgk | phosphoglycerate kinase (NCBI ptt file) | 110, 121 |
Cj1634c | aroC | chorismate synthase (NCBI ptt file) | 63, 110 |
Cj1642 | Cj1642 | hypothetical protein Cj1642 (NCBI ptt file) | 57, 160 |
Cj1672c | eno | enolase (NCBI ptt file) | 137, 160 |
Cj1673c | recA | recA protein (NCBI ptt file) | 38, 110 |
Cj1714 | Cj1714 | small hydrophobic protein (NCBI ptt file) | 11, 160 |
Cjt01 | tRNA-Leu | tRNA-Leu (NCBI) | 77, 110 |
Gene Page Help
Network Tab
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.
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For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.
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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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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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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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CircVis
Our 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;![](/static/images/help_images/circvis-help.png)
- 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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