Organism : Methanococcus maripaludis S2 | Module List :
Regulation information for MMP1085(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 MMP1085
Module neighborhood information for MMP1085
|Gene||Common Name||Description||Module membership|
|MMP0007||geranylgeranylglyceryl phosphate synthase-like protein||12, 143|
|MMP0034||GTP cyclohydrolase||130, 149|
|MMP0137||dys||putative deoxyhypusine synthase||25, 141, 149|
|MMP0145||hpt||adenine phosphoribosyltransferase||137, 143|
|MMP0153||aksA||trans-homoaconitate synthase||1, 143|
|MMP0178||purQ||phosphoribosylformylglycinamidine synthase I||95, 143|
|MMP0179||purL||phosphoribosylformylglycinamidine synthase||66, 143|
|MMP0187||thiC||thiamine biosynthesis protein ThiC||137, 143|
|MMP0264||MscMJ||mechanosensitive ion channel MscS||129, 143|
|MMP0284||infB||translation initiation factor IF-2||25, 149|
|MMP0319||cbiL||precorrin-2 C-20 methyltransferase||24, 140, 141, 149|
|MMP0320||shikimate kinase||47, 141|
|MMP0340||pycB||pyruvate carboxylase subunit B||24, 86, 120, 141, 149|
|MMP0415||O-sialoglycoprotein endopeptidase/protein kinase||47, 149|
|MMP0418||carbohydrate kinase PfkB||60, 137, 143|
|MMP0540||purC||phosphoribosylaminoimidazole-succinocarboxamide synthase||8, 112, 143|
|MMP0564||hypothetical protein MMP0564||111, 149|
|MMP0606||ribosomal RNA methyltransferase RrmJ/FtsJ||137, 143|
|MMP0607||nrpR||hypothetical protein MMP0607||115, 137, 143|
|MMP0694||beta-lactamase-like protein||51, 109, 149|
|MMP0697||leuS||leucyl-tRNA synthetase||8, 143|
|MMP0698||hypothetical protein MMP0698||21, 143|
|MMP0879||serS||seryl-tRNA synthetase||27, 143|
|MMP0880||aksF||isopropylmalate/isohomocitrate dehydrogenase||24, 60, 140, 143|
|MMP0905||hypothetical protein MMP0905||14, 149|
|MMP0906||ribonuclease Z||129, 149|
|MMP0907||transcriptional regulator TrmB||14, 149|
|MMP0919||dihydroorotate dehydrogenase electron transfer subunit||86, 141|
|MMP0920||ahcY||S-adenosyl-L-homocysteine hydrolase||80, 141|
|MMP0921||RNAse P, Rpr2/Rpp21 subunit||25, 141|
|MMP0941||hypothetical protein MMP0941||129, 149|
|MMP0953||cbiH||precorrin-3B C17-methyltransferase||24, 25, 149|
|MMP0989||top6B||DNA topoisomerase VI subunit B||139, 141|
|MMP1014||radical SAM domain-containing protein||25, 141|
|MMP1063||leuA||2-isopropylmalate synthase||81, 143|
|MMP1081||wbpG||putative LPS biosynthesis protein WbpG||137, 143|
|MMP1082||hisH||imidazole glycerol phosphate synthase subunit HisH||66, 143|
|MMP1083||imidazole glycerol phosphate synthase subunit HisF||137, 143|
|MMP1085||hypothetical protein MMP1085||141, 143, 149|
|MMP1086||hypothetical protein MMP1086||122, 141|
|MMP1107||Signal recognition particle protein SRP19||111, 141|
|MMP1108||corA||magnesium/cobalt transporter CorA||141, 149|
|MMP1112||hypothetical protein MMP1112||111, 129, 141, 149|
|MMP1122||translation-associated GTPase||137, 143|
|MMP1146||purF||amidophosphoribosyltransferase||7, 60, 137, 143|
|MMP1198||nitrate/sulfonate/bicarbonate ABC transporter ATPase||12, 143|
|MMP1307||methyltransferase-like protein||4, 149|
|MMP1313||fen-1||flap endonuclease-1||47, 52, 141|
|MMP1327||rpoK||RNA polymerase Rpb6||103, 139, 149|
|MMP1328||enolase||103, 139, 149|
|MMP1356||PP-loop domain-containing protein||25, 129, 139, 140, 149|
|MMP1357||hypothetical protein MMP1357||140, 149|
|MMP1361||rpoB2||DNA-directed RNA polymerase subunit beta''||25, 92, 109, 149|
|MMP1491||trzA||amidohydrolase||14, 111, 122, 149|
|MMP1492||pyrE||orotate phosphoribosyltransferase||14, 149|
|MMP1496||pheS||phenylalanyl-tRNA synthetase subunit alpha||137, 143|
|MMP1582||pdaD||pyruvoyl-dependent arginine decarboxylase||87, 149|
|MMP1592||trpS||tryptophanyl-tRNA synthetase||27, 143|
|MMP1594||hypothetical protein MMP1594||51, 143|
|MMP1614||hisS||histidyl-tRNA synthetase||141, 149|
|MMP1681||hypothetical protein MMP1681||21, 143|
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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- 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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