Organism : Methanococcus maripaludis S2 | Module List :
Regulation information for MMP0146(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 MMP0146
Module neighborhood information for MMP0146
|Gene||Common Name||Description||Module membership|
|MMP0026||DP2||DNA polymerase II large subunit||25, 41, 92|
|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|
|MMP0145||hpt||adenine phosphoribosyltransferase||137, 143|
|MMP0146||hypothetical protein MMP0146||17, 41, 137|
|MMP0147||nitrogenase reductase-like protein||17, 22|
|MMP0148||acsA||acetyl-CoA synthetase||17, 124|
|MMP0187||thiC||thiamine biosynthesis protein ThiC||137, 143|
|MMP0216||cation transport ATPase||4, 41, 95|
|MMP0348||GPR1/FUN34/yaaH family protein||17, 124|
|MMP0404||cofD||2-phospho-L-lactate transferase||87, 137|
|MMP0418||carbohydrate kinase PfkB||60, 137, 143|
|MMP0493||cobN||cobaltochelatase subunit CobN||41, 44|
|MMP0606||ribosomal RNA methyltransferase RrmJ/FtsJ||137, 143|
|MMP0607||nrpR||hypothetical protein MMP0607||115, 137, 143|
|MMP0610||tgtA||7-cyano-7-deazaguanine tRNA-ribosyltransferase||25, 41|
|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|
|MMP0881||hypothetical protein MMP0881||111, 137|
|MMP0977||CooC||CO dehydrogenase maturation factor||17, 124|
|MMP0978||hypothetical protein MMP0978||17, 124|
|MMP0979||hypothetical protein MMP0979||17, 124|
|MMP0980||cdh||acetyl-CoA decarbonylase/synthase complex subunit gamma||17, 124|
|MMP0981||cdhD||acetyl-CoA decarbonylase/synthase complex subunit delta||17, 124|
|MMP0982||hypothetical protein MMP0982||17, 124|
|MMP0983||cdhB||acetyl-CoA decarbonylase/synthase complex subunit beta||17, 124|
|MMP0984||cdh||acetyl-CoA decarbonylase/synthase complex subunit epsilon||10, 17|
|MMP0985||cdhA||acetyl-CoA decarbonylase/synthase complex subunit alpha||10, 17|
|MMP1074||ehbD||hypothetical protein MMP1074||17, 106|
|MMP1081||wbpG||putative LPS biosynthesis protein WbpG||137, 143|
|MMP1083||imidazole glycerol phosphate synthase subunit HisF||137, 143|
|MMP1105||sucC||succinate-CoA ligase (ADP-forming), beta chain||7, 81, 137|
|MMP1106||hypothetical protein MMP1106||81, 137, 140|
|MMP1122||translation-associated GTPase||137, 143|
|MMP1146||purF||amidophosphoribosyltransferase||7, 60, 137, 143|
|MMP1150||mtaA||uroporphyrinogen decarboxylase||4, 41, 95|
|MMP1200||lysA||diaminopimelate decarboxylase||21, 41|
|MMP1206||glnA||glutamine synthetase||99, 137|
|MMP1271||vorA||2-oxoisovalerate oxidoreductase subunit alpha||10, 17|
|MMP1274||AMP-dependent synthetase and ligase||10, 17|
|MMP1316||korB||2-oxoglutarate ferredoxin oxidoreductase subunit beta||7, 120, 137|
|MMP1334||solute-binding protein/glutamate receptor||41, 129|
|MMP1440||tRNA-modifying protein||129, 137|
|MMP1441||mobB||putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein||41, 89|
|MMP1468||hypothetical protein MMP1468||17, 124|
|MMP1496||pheS||phenylalanyl-tRNA synthetase subunit alpha||137, 143|
|MMP1502||porF||hypothetical protein MMP1502||10, 17|
|MMP1503||porE||pyruvate oxidoreductase-associated||10, 17|
|MMP1504||porB||pyruvate ferredoxin oxidoreductase subunit beta||10, 17|
|MMP1505||porA||pyruvate oxidoreductase (synthase) subunit alpha||10, 17|
|MMP1506||porD||pyruvate oxidoreductase (synthase) subunit delta||10, 17|
|MMP1507||porC||pyruvate ferredoxin oxidoreductase subunit gamma||10, 17|
|MMP1532||pgk||phosphoglycerate kinase||120, 137|
|MMP1612||hypothetical protein MMP1612||41, 95|
|MMP1651||modA||molybdenum ABC transporter periplasmic molybdate-binding protein||41, 95|
|MMP1656||glutamine amidotransferase subunit PdxT||8, 137|
|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.
You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".
For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.
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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