Organism : Methanococcus maripaludis S2 | Module List :
Regulation information for MMP1700(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 MMP1700
Module neighborhood information for MMP1700
|Gene||Common Name||Description||Module membership|
|MMP0026||DP2||DNA polymerase II large subunit||25, 41, 92|
|MMP0087||hmgA||hydroxymethylglutaryl-coenzyme A reductase:3-hydroxy-3-methylglutaryl coenzyme A reductase||39, 136|
|MMP0088||hemA||glutamyl-tRNA reductase||39, 136|
|MMP0096||putative GntR family transcriptional regulator||39, 58|
|MMP0108||ABC-type Iron(III)-binding periplasmic protein precursor||41, 67, 95|
|MMP0141||hypothetical protein MMP0141||41, 51|
|MMP0142||thiamine pyrophosphate dependent protein||17, 41, 51|
|MMP0144||hpcE||5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase||17, 41|
|MMP0146||hypothetical protein MMP0146||17, 41, 137|
|MMP0164||cbiX(s)||sirohydrochlorin cobaltochelatase||39, 136|
|MMP0216||cation transport ATPase||4, 41, 95|
|MMP0242||hypothetical protein MMP0242||8, 39, 96|
|MMP0388||geranylgeranyl reductase||39, 68|
|MMP0493||cobN||cobaltochelatase subunit CobN||41, 44|
|MMP0610||tgtA||7-cyano-7-deazaguanine tRNA-ribosyltransferase||25, 41|
|MMP0629||hypothetical protein MMP0629||8, 39|
|MMP0644||cation diffusion facilitator family transporter||39, 136|
|MMP0645||mdh||malate dehydrogenase||8, 39, 136|
|MMP0646||hypothetical protein MMP0646||39, 136|
|MMP0650||ilvB||acetolactate synthase catalytic subunit||8, 39|
|MMP0651||ilvH||acetolactate synthase 3 regulatory subunit||8, 39|
|MMP0670||hypothetical protein MMP0670||41, 51|
|MMP0861||kamA||lysine 2,3-aminomutase||41, 95|
|MMP0862||yodP||GCN5-like N-acetyltransferase||41, 95|
|MMP0866||proX||glycine betaine ABC transporter substrate-binding protein||41, 89|
|MMP0867||binding-protein dependent transport system inner membrane protein||41, 89|
|MMP0868||proV||ABC transporter ATPase||41, 66|
|MMP0874||SAM-binding motif-containing protein||39, 136|
|MMP0875||slpB||S layer protein||39, 136|
|MMP0884||hypothetical protein MMP0884||39, 51|
|MMP0888||cobalt transport protein CbiN||39, 136|
|MMP0889||cobalt transport protein CbiM||39, 136|
|MMP0965||formylmethanofuran dehydrogenase subunit E-like protein||8, 39, 136|
|MMP1150||mtaA||uroporphyrinogen decarboxylase||4, 41, 95|
|MMP1176||putative iron transport system substrate-binding protein, N-term half||39, 136|
|MMP1177||putative iron transport system substrate-binding protein, C-term half||39, 136|
|MMP1178||periplasmic binding protein||39, 136|
|MMP1181||iron transport system binding protein||39, 136|
|MMP1182||transport system permease||39, 136|
|MMP1183||iron ABC transporter ATPase subunit||39, 136|
|MMP1200||lysA||diaminopimelate decarboxylase||21, 41|
|MMP1334||solute-binding protein/glutamate receptor||41, 129|
|MMP1437||top6A||DNA topoisomerase VI subunit A||39, 112|
|MMP1441||mobB||putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein||41, 89|
|MMP1612||hypothetical protein MMP1612||41, 95|
|MMP1651||modA||molybdenum ABC transporter periplasmic molybdate-binding protein||41, 95|
|MMP1700||SSS sodium solute transporter superfamily||39, 41|
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
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