Organism : Methanococcus maripaludis S2 | Module List :
Regulation information for MMP0653(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 MMP0653
Module neighborhood information for MMP0653
|Gene||Common Name||Description||Module membership|
|MMP0059||hypothetical protein MMP0059||8, 58, 64|
|MMP0174||HD phosphohydrolase family protein||42, 131|
|MMP0188||diphthamide biosynthesis protein||42, 163|
|MMP0208||hypothetical protein MMP0208||26, 31, 42, 82|
|MMP0228||trm1||N(2),N(2)-dimethylguanosine tRNA methyltransferase||21, 42|
|MMP0295||thrB||homoserine kinase||64, 90|
|MMP0315||iorB1||indolepyruvate oxidoreductase subunit B||25, 64|
|MMP0316||iorA1||indolepyruvate oxidoreductase subunit alpha 1||25, 64, 87|
|MMP0361||hypothetical protein MMP0361||42, 45, 163|
|MMP0368||hypothetical protein MMP0368||64, 163|
|MMP0429||hypothetical protein MMP0429||64, 136|
|MMP0436||rimK||RimK domain-containing protein||6, 31, 42, 72, 82, 110|
|MMP0437||hypothetical protein MMP0437||6, 31, 42, 53, 82|
|MMP0473||hypothetical protein MMP0473||31, 42|
|MMP0495||hypothetical protein MMP0495||31, 42, 127, 155|
|MMP0522||hypothetical protein MMP0522||42, 85, 146, 153|
|MMP0523||ABC transporter ATP-binding protein||42, 85, 146, 153|
|MMP0565||hypothetical protein MMP0565||42, 85|
|MMP0653||bile acid:sodium symporter||42, 64|
|MMP0756||hypothetical protein MMP0756||42, 166|
|MMP0761||hypothetical protein MMP0761||22, 64|
|MMP0766||resP||site-specific recombinase||6, 42, 53, 72, 127|
|MMP0772||hypothetical protein MMP0772||42, 123|
|MMP0775||hypothetical protein MMP0775||42, 146, 153, 163|
|MMP0777||hypothetical protein MMP0777||42, 62|
|MMP0796||sugar efflux transporter||36, 42, 53, 69|
|MMP0807||carboxymuconolactone decarboxylase-like protein||42, 85, 155|
|MMP0831||mtbA||methylcobalamin:coenzyme M methyltransferase||42, 82|
|MMP0834||mtbA||uroporphyrinogen decarboxylase||26, 36, 42, 72, 155|
|MMP0869||cytidine/deoxycytidylate deaminase||42, 155|
|MMP0892||GCN5-like N-acetyltransferase||42, 85|
|MMP0975||modA||molybdenum ABC transporter solute-binding protein||64, 92|
|MMP1020||hypothetical protein MMP1020||42, 45|
|MMP1079||glycosyl transferase family protein||64, 67|
|MMP1119||yjlA||hypothetical protein MMP1119||64, 163|
|MMP1123||radical SAM domain-containing protein||64, 67|
|MMP1226||geranylgeranyl reductase||42, 64|
|MMP1280||hypothetical protein MMP1280||42, 62|
|MMP1379||thyA||thymidylate synthase||64, 92|
|MMP1389||hypothetical protein MMP1389||42, 163|
|MMP1476||hypothetical protein MMP1476||42, 45|
|MMP1536||hypothetical protein MMP1536||36, 42, 53, 161|
|MMP1596||hypothetical protein MMP1596||31, 42, 155|
|MMP1620||hypothetical protein MMP1620||42, 53|
|MMP1655||hypothetical protein MMP1655||36, 42, 163|
|MMP1660||hypothetical protein MMP1660||42, 108, 123, 131|
|MMP1664||hypothetical protein MMP1664||42, 146|
|MMP1678||nfo||endonuclease IV||42, 72, 82|
|RNA_34||tRNA-Met4||Met tRNA||42, 100|
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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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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