Organism : Methanococcus maripaludis S2 | Module List :
Regulation information for MMP1317(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|
Module neighborhood information for MMP1317
|Gene||Common Name||Description||Module membership|
|MMP0038||type II secretion system protein||115, 160|
|MMP0039||hypothetical protein MMP0039||115, 160|
|MMP0040||type II secretion system protein E||115, 160|
|MMP0118||beta-lactamase domain-containing protein||115, 133|
|MMP0165||ABC transporter||28, 115|
|MMP0228||trm1||N(2),N(2)-dimethylguanosine tRNA methyltransferase||21, 42|
|MMP0233||hypothetical protein MMP0233||38, 115|
|MMP0270||Fe-S cluster domain-containing protein||21, 70|
|MMP0271||putative ATP binding nickel incorporation protein||21, 95|
|MMP0272||ABC transporter ATPase||21, 70|
|MMP0273||comA||phosphosulfolactate synthase||21, 70|
|MMP0403||hypothetical protein MMP0403||87, 115|
|MMP0579||hypothetical protein MMP0579||115, 139|
|MMP0580||act||anaerobic ribonucleoside-triphosphate reductase activating protein||115, 129|
|MMP0607||nrpR||hypothetical protein MMP0607||115, 137, 143|
|MMP0618||hypothetical protein MMP0618||21, 70|
|MMP0619||hypothetical protein MMP0619||21, 70|
|MMP0620||atwA||methyl coenzyme M reductase, component A2||21, 70|
|MMP0632||ATP/GTP-binding motif-containing protein||19, 115|
|MMP0666||Na/Pi-cotransporter II-like protein||7, 115|
|MMP0689||xanthine/uracil permease family protein||38, 115|
|MMP0698||hypothetical protein MMP0698||21, 143|
|MMP0865||aminotransferase (subgroup II) adenosylmethionine-8-amino-7-oxononanoate aminotransferase||115, 140|
|MMP0883||hypothetical protein MMP0883||115, 129|
|MMP0904||selD||selenophosphate synthetase||21, 70|
|MMP0918||asnB||glutamine-hydrolyzing asparagine synthase||49, 115|
|MMP0942||hypothetical protein MMP0942||111, 115|
|MMP0948||hypothetical protein MMP0948||4, 115|
|MMP0954||hypothetical protein MMP0954||21, 70|
|MMP0969||hypothetical protein MMP0969||106, 115|
|MMP1021||hypothetical protein MMP1021||8, 21|
|MMP1022||hypothetical protein MMP1022||21, 70|
|MMP1023||TetR family transcriptional regulator||8, 21, 78|
|MMP1026||argS||arginyl-tRNA synthetase||12, 21|
|MMP1069||basic helix-loop-helix dimerization domain-containing protein||106, 115|
|MMP1186||lon||thiol (cysteine) protease||21, 115|
|MMP1200||lysA||diaminopimelate decarboxylase||21, 41|
|MMP1259||FAD-dependent pyridine nucleotide-disulfide oxidoreductase||12, 21|
|MMP1279||camphor resistance protein CrcB||115, 160|
|MMP1290||GTP-binding protein||49, 115|
|MMP1317||hypothetical protein MMP1317||21, 115|
|MMP1318||lysS||lysyl-tRNA synthetase||20, 21|
|MMP1430||cation transporter||49, 115|
|MMP1471||hypothetical protein MMP1471||38, 115|
|MMP1512||alr||alanine racemase||8, 21|
|MMP1513||ald||alanine dehydrogenase||8, 21|
|MMP1527||aspartate aminotransferase||8, 21|
|MMP1583||S-adenosylmethionine decarboxylase-like protein||21, 112|
|MMP1584||spermidine synthase||11, 21|
|MMP1611||hypothetical protein MMP1611||21, 106|
|MMP1657||hypothetical protein MMP1657||21, 28|
|MMP1681||hypothetical protein MMP1681||21, 143|
|MMP1682||recJ||single stranded DNA-specific exonuclease||21, 106|
|MMP1704||hypothetical protein MMP1704||21, 115|
|MMP1706||H/ACA RNA-protein complex component Nop10p||20, 21|
|MMP1707||aIF2_alpha||translation initiation factor IF-2 subunit alpha||20, 21|
|MMP1711||pcnA||proliferating cell nuclear antigen||115, 139|
|MMP1722||hisF||imidazole glycerol phosphate synthase subunit HisF||111, 115|
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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