Organism : Methanococcus maripaludis S2 | Module List :
Regulation information for MMP0843(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 MMP0843
|Gene||Common Name||Description||Module membership|
|MMP0008||DP1||DNA polymerase II small subunit||22, 75, 142|
|MMP0072||hypothetical protein MMP0072||28, 129|
|MMP0085||hypothetical protein MMP0085||22, 106|
|MMP0147||nitrogenase reductase-like protein||17, 22|
|MMP0165||ABC transporter||28, 115|
|MMP0166||MATE family drug/sodium antiporter||1, 28|
|MMP0167||ABC transporter ATP-binding protein||1, 28|
|MMP0168||ParR family transcriptional regulator||1, 28|
|MMP0256||hisH||imidazole glycerol phosphate synthase subunit HisH||28, 58|
|MMP0257||tbp||transcription factor||28, 58|
|MMP0265||hypothetical protein MMP0265||28, 129|
|MMP0304||N-glycosylase/DNA lyase||22, 33, 43, 152|
|MMP0313||hypothetical protein MMP0313||28, 73|
|MMP0342||hypothetical protein MMP0342||28, 98|
|MMP0453||neutral zinc metallopeptidase||22, 75|
|MMP0499||hypothetical protein MMP0499||22, 28, 144, 146, 153|
|MMP0511||fmdB||molybdenum containing formylmethanofuran dehydrogenase subunit B||5, 28|
|MMP0536||hypothetical protein MMP0536||1, 28|
|MMP0547||RecJ-like protein||22, 166|
|MMP0570||hypothetical protein MMP0570||22, 65|
|MMP0587||napA||sodium/hydrogen exchanger||22, 69|
|MMP0608||2-hydroxyglutaryl-CoA dehydratase subunit A-like protein||1, 28|
|MMP0630||feoB||ferrous iron transporter||28, 76, 106, 121|
|MMP0631||putative iron dependent repressor||28, 121, 144|
|MMP0684||hsp20||heat shock protein Hsp20||28, 121|
|MMP0717||hypothetical protein MMP0717||22, 144|
|MMP0760||hypothetical protein MMP0760||22, 67, 92|
|MMP0761||hypothetical protein MMP0761||22, 64|
|MMP0792||membrane protein||9, 22|
|MMP0793||hypothetical protein MMP0793||9, 22|
|MMP0795||hypothetical protein MMP0795||22, 126|
|MMP0812||hypothetical protein MMP0812||12, 28|
|MMP0843||hypothetical protein MMP0843||22, 28|
|MMP0871||hypothetical protein MMP0871||22, 153, 166|
|MMP0991||hypothetical protein MMP0991||22, 65|
|MMP1051||surE||stationary phase survival protein SurE||12, 28, 106|
|MMP1059||hypothetical protein MMP1059||2, 22, 33|
|MMP1066||putative molybdenum cofactor biosynthesis protein MoaC||28, 133|
|MMP1171||pssA||CDP-diacylglycerol--serine O-phosphatidyltransferase||28, 66|
|MMP1228||hypothetical protein MMP1228||4, 22, 142|
|MMP1236||hypothetical protein MMP1236||22, 55, 117, 142, 152|
|MMP1265||glutamyl-tRNA(Gln) amidotransferase subunit E||28, 129|
|MMP1303||sensory transduction histidine kinase||4, 28, 66|
|MMP1398||dapE||diaminopimelate aminotransferase||22, 142|
|MMP1447||Cro repressor family protein||22, 117|
|MMP1452||ehaE||hypothetical protein MMP1452||22, 117|
|MMP1453||ehaF||hypothetical protein MMP1453||22, 117|
|MMP1467||ehaT||hypothetical protein MMP1467||28, 129, 133|
|MMP1573||bioD||dethiobiotin synthase||28, 106|
|MMP1580||dihydropteroate synthase||22, 145, 152|
|MMP1597||phosphatidylglycerophosphatase A||22, 142, 144|
|MMP1636||major facilitator transporter||22, 65, 153|
|MMP1657||hypothetical protein MMP1657||21, 28|
|MMP1686||cbf5||H/ACA RNA-protein complex component Cbf5p||22, 67|
|Unanno_59||None||28, 104, 133|
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
- 3. Target genes (other module members)
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