Organism : Methanococcus maripaludis S2 | Module List :
Regulation information for MMP1549(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 MMP1549
Module neighborhood information for MMP1549
|Gene||Common Name||Description||Module membership|
|MMP0071||DNA primase small subunit||72, 152|
|MMP0117||hypothetical protein MMP0117||94, 145|
|MMP0119||birA||biotin--acetyl-CoA-carboxylase ligase||1, 75, 142|
|MMP0153||aksA||trans-homoaconitate synthase||1, 143|
|MMP0154||hypothetical protein MMP0154||1, 13|
|MMP0166||MATE family drug/sodium antiporter||1, 28|
|MMP0167||ABC transporter ATP-binding protein||1, 28|
|MMP0168||ParR family transcriptional regulator||1, 28|
|MMP0176||cell division protein CDC48||1, 46|
|MMP0177||hypothetical protein MMP0177||83, 117, 152|
|MMP0180||ribC||riboflavin synthase||1, 58|
|MMP0231||cysteine-rich small domain||145, 152|
|MMP0239||hypothetical protein MMP0239||1, 49, 75, 106|
|MMP0269||hypothetical protein MMP0269||76, 152|
|MMP0276||hypothetical protein MMP0276||65, 94|
|MMP0304||N-glycosylase/DNA lyase||22, 33, 43, 152|
|MMP0312||hypothetical protein MMP0312||73, 94|
|MMP0327||deoA||thymidine phosphorylase||94, 152|
|MMP0336||hjc||Holliday junction resolvase||13, 94|
|MMP0337||hypothetical protein MMP0337||13, 94|
|MMP0431||rhodopsin-like GPCR superfamily protein||94, 145|
|MMP0432||TatD-like deoxyribonuclease||94, 145|
|MMP0433||putative flavodoxin||94, 145|
|MMP0451||hypothetical protein MMP0451||1, 70|
|MMP0536||hypothetical protein MMP0536||1, 28|
|MMP0548||hisB||imidazoleglycerol-phosphate dehydratase||94, 145|
|MMP0549||hypothetical protein MMP0549||94, 145|
|MMP0585||UspA domain-containing protein||83, 151, 152|
|MMP0599||cbiJ||precorrin-6x reductase CbiJ/CobK||33, 152|
|MMP0608||2-hydroxyglutaryl-CoA dehydratase subunit A-like protein||1, 28|
|MMP0660||apt||adenine phosphoribosyltransferase||83, 94, 152|
|MMP0676||intermediate filament protein||145, 152|
|MMP0677||hypothetical protein MMP0677||94, 145|
|MMP0685||N-6 adenine-specific DNA methylase||1, 144|
|MMP0876||cofG||FO synthase subunit 1||1, 129|
|MMP1029||hypothetical protein MMP1029||65, 152|
|MMP1065||BadM/Rrf2 family transcriptional regulator||55, 152|
|MMP1071||hypothetical protein MMP1071||1, 106|
|MMP1072||aminotransferase (subgroup I) aromatic aminotransferase||1, 106|
|MMP1145||minD||septum formation inhibitor-activating ATPase||94, 145|
|MMP1185||hydrogen uptake protein:hydrogenase maturation protease HycI||1, 46|
|MMP1233||formate dehydrogenase family accessory protein FdhD||145, 152|
|MMP1236||hypothetical protein MMP1236||22, 55, 117, 142, 152|
|MMP1238||bioB||biotin synthase||1, 153|
|MMP1240||Sep-tRNA:Cys-tRNA synthetase||1, 55|
|MMP1241||hypothetical protein MMP1241||1, 55, 94, 117|
|MMP1372||manB||phosphomannomutase||49, 94, 152|
|MMP1477||cbiA||cobyrinic acid a,c-diamide synthase||46, 152|
|MMP1487||gapN||aldehyde dehydrogenase||55, 152|
|MMP1548||Fe-S type hydro-lyase tartrate/fumarate subunit beta||94, 145|
|MMP1549||AP endonuclease||1, 94, 152|
|MMP1550||NADP oxidoreductase, coenzyme F420-dependent||1, 58|
|MMP1580||dihydropteroate synthase||22, 145, 152|
|MMP1605||pyruvate kinase||1, 54, 146, 166|
|MMP1606||flavoprotein:DNA/pantothenate metabolism flavoprotein||1, 13, 49|
|MMP1619||molybdenum cofactor biosynthesis protein MoeA||117, 152|
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.
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;
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