Organism : Methanococcus maripaludis S2 | Module List :
hypothetical protein MMP0307
Functional Annotations (1)
|zinc ion binding||go/ molecular_function|
Regulation information for MMP0307(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 6 motifs predicted.
|Motif Id||e-value||Consensus||Motif Logo|
Functional Enrichment for MMP0307
|zinc ion binding||go/ molecular_function|
Module neighborhood information for MMP0307
|Gene||Common Name||Description||Module membership|
|Antisense_24||None||5, 49, 90|
|MMP0020||nickel responsive regulator||49, 123|
|MMP0036||tfe||transcription initiation factor E subunit alpha||49, 87, 92, 129|
|MMP0063||argB||acetylglutamate kinase||49, 151|
|MMP0084||hypothetical protein MMP0084||49, 106|
|MMP0128||cyclase family protein||73, 146, 153|
|MMP0193||hypothetical protein MMP0193||144, 153|
|MMP0207||modC||molybdenum ABC transporter ATP-binding protein||57, 153|
|MMP0239||hypothetical protein MMP0239||1, 49, 75, 106|
|MMP0268||truA||tRNA pseudouridine synthase A||49, 51|
|MMP0277||TraB family protein||49, 90|
|MMP0279||mptG||beta-ribofuranosylaminobenzene 5'-phosphate synthase family protein||49, 90|
|MMP0302||hypothetical protein MMP0302||49, 90|
|MMP0304||N-glycosylase/DNA lyase||22, 33, 43, 152|
|MMP0305||2-oxoacid ferredoxin oxidoreductase subunit beta||2, 33, 43|
|MMP0306||oxidoreductase family protein member subunit alpha||2, 33, 43|
|MMP0307||hypothetical protein MMP0307||33, 49, 153|
|MMP0311||hypothetical protein MMP0311||33, 73|
|MMP0426||nitroreductase family protein||57, 102, 106, 153|
|MMP0499||hypothetical protein MMP0499||22, 28, 144, 146, 153|
|MMP0522||hypothetical protein MMP0522||42, 85, 146, 153|
|MMP0523||ABC transporter ATP-binding protein||42, 85, 146, 153|
|MMP0524||hypothetical protein MMP0524||4, 58, 146, 153, 163|
|MMP0527||hypothetical protein MMP0527||76, 153|
|MMP0562||hypothetical protein MMP0562||49, 124|
|MMP0599||cbiJ||precorrin-6x reductase CbiJ/CobK||33, 152|
|MMP0600||hypothetical protein MMP0600||2, 33|
|MMP0643||hypothetical protein MMP0643||49, 65|
|MMP0691||hypothetical protein MMP0691||33, 73|
|MMP0693||aminoacyl-tRNA synthetase, class II||33, 54|
|MMP0725||putative integral membrane protein||49, 75, 90, 151|
|MMP0727||uvrB||excinuclease ABC subunit B||49, 142|
|MMP0742||hypothetical protein MMP0742||23, 49|
|MMP0775||hypothetical protein MMP0775||42, 146, 153, 163|
|MMP0871||hypothetical protein MMP0871||22, 153, 166|
|MMP0902||hypothetical protein MMP0902||12, 49, 55|
|MMP0903||hypothetical protein MMP0903||33, 54, 55|
|MMP0918||asnB||glutamine-hydrolyzing asparagine synthase||49, 115|
|MMP0994||hypothetical protein MMP0994||67, 144, 153|
|MMP1059||hypothetical protein MMP1059||2, 22, 33|
|MMP1060||cysS||cysteinyl-tRNA synthetase||33, 102|
|MMP1202||hypothetical protein MMP1202||104, 153|
|MMP1203||cbiD||cobalt-precorrin-6A synthase||104, 153|
|MMP1218||hypothetical protein MMP1218||12, 46, 49|
|MMP1234||UBA/THIF-type NAD/FAD binding protein||33, 54, 55, 106|
|MMP1235||moaE||molybdopterin biosynthesis MoaE||49, 55, 106, 117, 150|
|MMP1238||bioB||biotin synthase||1, 153|
|MMP1282||hypothetical protein MMP1282||49, 102, 106, 150|
|MMP1283||hypothetical protein MMP1283||49, 102, 150|
|MMP1290||GTP-binding protein||49, 115|
|MMP1343||hypothetical protein MMP1343||49, 151|
|MMP1345||undecaprenyl pyrophospahte synthetase-like protein||49, 111|
|MMP1346||basic helix-loop-helix dimerization domain-containing protein||49, 67, 142|
|MMP1372||manB||phosphomannomutase||49, 94, 152|
|MMP1387||hypothetical protein MMP1387||33, 73, 150|
|MMP1430||cation transporter||49, 115|
|MMP1431||2pgk||2-phosphoglycerate kinase||49, 51|
|MMP1494||hypothetical protein MMP1494||104, 153|
|MMP1551||ffh||signal recognition particle protein Srp54||49, 55, 83|
|MMP1578||nicotinamide-nucleotide adenylyltransferase||144, 153|
|MMP1606||flavoprotein:DNA/pantothenate metabolism flavoprotein||1, 13, 49|
|MMP1607||hypothetical protein MMP1607||49, 55, 83|
|MMP1636||major facilitator transporter||22, 65, 153|
|MMP1683||hypothetical protein MMP1683||33, 73|
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.
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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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