Organism : Methanococcus maripaludis S2 | Module List :
Regulation information for MMP0999(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 MMP0999
Module neighborhood information for MMP0999
|Gene||Common Name||Description||Module membership|
|MMP0046||hypothetical protein MMP0046||20, 51, 140|
|MMP0074||hypothetical protein MMP0074||51, 140|
|MMP0106||hypothetical protein MMP0106||107, 140|
|MMP0108||ABC-type Iron(III)-binding periplasmic protein precursor||41, 67, 95|
|MMP0133||guaB||inosine-5'-monophosphate dehydrogenase||25, 120, 140|
|MMP0178||purQ||phosphoribosylformylglycinamidine synthase I||95, 143|
|MMP0210||hypothetical protein MMP0210||58, 140|
|MMP0216||cation transport ATPase||4, 41, 95|
|MMP0220||Sodium/proline symporter-related||70, 140|
|MMP0224||hemL||glutamate-1-semialdehyde aminotransferase||60, 130, 140|
|MMP0253||acd||CoA-binding domain-containing protein||95, 124|
|MMP0271||putative ATP binding nickel incorporation protein||21, 95|
|MMP0282||purE||phosphoribosylaminoimidazole carboxylase catalytic subunit||7, 140|
|MMP0319||cbiL||precorrin-2 C-20 methyltransferase||24, 140, 141, 149|
|MMP0346||2-hydroxyglutaryl-CoA dehydratase subunit D-like protein||7, 140|
|MMP0354||putative oligosaccharide transporter||80, 95|
|MMP0356||group 1 glycosyl transferase||80, 139, 140|
|MMP0479||hypothetical protein MMP0479||4, 95|
|MMP0530||hypothetical protein MMP0530||92, 140|
|MMP0531||hypothetical protein MMP0531||106, 140|
|MMP0541||serB||phosphoserine phosphatase SerB||7, 40, 139, 140|
|MMP0550||amino acid ABC transporter periplasmic protein||81, 140|
|MMP0554||SAM-binding motif-containing protein||129, 140|
|MMP0588||dph5||diphthine synthase||25, 81, 140|
|MMP0609||pth2||peptidyl-tRNA hydrolase||66, 140|
|MMP0705||wbpI||UDP-N-acetylglucosamine 2-epimerase||80, 140|
|MMP0707||sodium/hydrogen exchanger||87, 109, 140|
|MMP0849||L-lysine/ homoserine-homoserine lactone exporter family protein||95, 117|
|MMP0861||kamA||lysine 2,3-aminomutase||41, 95|
|MMP0862||yodP||GCN5-like N-acetyltransferase||41, 95|
|MMP0865||aminotransferase (subgroup II) adenosylmethionine-8-amino-7-oxononanoate aminotransferase||115, 140|
|MMP0873||hypothetical protein MMP0873||95, 107|
|MMP0878||ribonuclease P-like protein||25, 87, 140|
|MMP0880||aksF||isopropylmalate/isohomocitrate dehydrogenase||24, 60, 140, 143|
|MMP0999||hypothetical protein MMP0999||95, 140|
|MMP1000||hypothetical protein MMP1000||4, 95|
|MMP1068||K+-dependent Na+/Ca+ exchanger related-protein:Sodium/calcium exchanger membrane region||81, 140|
|MMP1099||phosphate transporter PhoU||66, 89, 95|
|MMP1106||hypothetical protein MMP1106||81, 137, 140|
|MMP1150||mtaA||uroporphyrinogen decarboxylase||4, 41, 95|
|MMP1199||phosphate transporter PhoU||95, 133|
|MMP1210||hypothetical protein MMP1210||89, 95|
|MMP1212||acetyl-CoA acetyltransferase||89, 95|
|MMP1219||putative dinG ATP-dependent helicase||95, 107|
|MMP1232||PP-loop domain-containing protein||95, 104|
|MMP1312||hypothetical protein MMP1312||52, 140|
|MMP1326||rpoN||DNA-directed RNA polymerase subunit N||103, 118, 140|
|MMP1337||hydrogenase maturation protease||95, 107|
|MMP1353||hypothetical protein MMP1353||81, 140|
|MMP1356||PP-loop domain-containing protein||25, 129, 139, 140, 149|
|MMP1357||hypothetical protein MMP1357||140, 149|
|MMP1362||rpoB1||DNA-directed RNA polymerase subunit B'||63, 130, 140|
|MMP1425||tRNA 2'-O-methylase||25, 87, 140|
|MMP1426||dcd||bifunctional dCTP deaminase/dUTP diphosphatase||16, 112, 140|
|MMP1429||rpm||DNA-directed RNA polymerase subunit M||95, 107|
|MMP1438||hypothetical protein MMP1438||14, 140|
|MMP1466||ehaS||putative CBS domain-containing signal transduction protein||95, 107, 133|
|MMP1540||hypothetical protein MMP1540||24, 140|
|MMP1612||hypothetical protein MMP1612||41, 95|
|MMP1651||modA||molybdenum ABC transporter periplasmic molybdate-binding protein||41, 95|
|MMP1652||molybdate ABC transporter periplasmic substrate-binding protein||89, 95|
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.
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