Organism : Methanococcus maripaludis S2 | Module List :
Regulation information for MMP0479(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 MMP0479
|Gene||Common Name||Description||Module membership|
|MMP0011||DNA-cytosine methyltransferase||4, 104|
|MMP0105||hypothetical protein MMP0105||4, 107|
|MMP0108||ABC-type Iron(III)-binding periplasmic protein precursor||41, 67, 95|
|MMP0140||(NiFe) hydrogenase maturation protein HypF||4, 85|
|MMP0178||purQ||phosphoribosylformylglycinamidine synthase I||95, 143|
|MMP0181||hypothetical protein MMP0181||4, 58|
|MMP0216||cation transport ATPase||4, 41, 95|
|MMP0243||hypothetical protein MMP0243||4, 25, 38|
|MMP0253||acd||CoA-binding domain-containing protein||95, 124|
|MMP0271||putative ATP binding nickel incorporation protein||21, 95|
|MMP0296||hypothetical protein MMP0296||4, 129|
|MMP0333||hypothetical protein MMP0333||4, 126|
|MMP0354||putative oligosaccharide transporter||80, 95|
|MMP0392||purD||phosphoribosylamine--glycine ligase||4, 75, 104|
|MMP0401||metE||methionine synthase||4, 15, 80|
|MMP0412||MiaB-like tRNA modifying protein||4, 25, 87|
|MMP0447||nitrogenase-like protein||4, 146|
|MMP0448||hypothetical protein MMP0448||4, 70|
|MMP0479||hypothetical protein MMP0479||4, 95|
|MMP0503||hypothetical protein MMP0503||4, 126|
|MMP0524||hypothetical protein MMP0524||4, 58, 146, 153, 163|
|MMP0525||hypothetical protein MMP0525||4, 146, 163|
|MMP0571||moaA||molybdenum cofactor biosynthesis protein A||4, 89|
|MMP0849||L-lysine/ homoserine-homoserine lactone exporter family protein||95, 117|
|MMP0861||kamA||lysine 2,3-aminomutase||41, 95|
|MMP0862||yodP||GCN5-like N-acetyltransferase||41, 95|
|MMP0873||hypothetical protein MMP0873||95, 107|
|MMP0886||cobalt ABC transporter inner membrane protein||4, 151|
|MMP0948||hypothetical protein MMP0948||4, 115|
|MMP0949||tRNA CCA-pyrophosphorylase||4, 70|
|MMP0999||hypothetical protein MMP0999||95, 140|
|MMP1000||hypothetical protein MMP1000||4, 95|
|MMP1064||adenylate cyclase||4, 51|
|MMP1099||phosphate transporter PhoU||66, 89, 95|
|MMP1130||hypothetical protein MMP1130||4, 38|
|MMP1150||mtaA||uroporphyrinogen decarboxylase||4, 41, 95|
|MMP1199||phosphate transporter PhoU||95, 133|
|MMP1210||hypothetical protein MMP1210||89, 95|
|MMP1212||acetyl-CoA acetyltransferase||89, 95|
|MMP1219||putative dinG ATP-dependent helicase||95, 107|
|MMP1228||hypothetical protein MMP1228||4, 22, 142|
|MMP1232||PP-loop domain-containing protein||95, 104|
|MMP1303||sensory transduction histidine kinase||4, 28, 66|
|MMP1304||response regulator receiver protein||4, 126|
|MMP1305||hypothetical protein MMP1305||4, 126|
|MMP1307||methyltransferase-like protein||4, 149|
|MMP1337||hydrogenase maturation protease||95, 107|
|MMP1429||rpm||DNA-directed RNA polymerase subunit M||95, 107|
|MMP1466||ehaS||putative CBS domain-containing signal transduction protein||95, 107, 133|
|MMP1612||hypothetical protein MMP1612||41, 95|
|MMP1645||aspartate/glutamate/uridylate kinase||4, 126|
|MMP1651||modA||molybdenum ABC transporter periplasmic molybdate-binding protein||41, 95|
|MMP1652||molybdate ABC transporter periplasmic substrate-binding protein||89, 95|
|MMP1698||hypothetical protein MMP1698||4, 8|
|RNA_17||tRNA-Pro2||Pro tRNA||4, 100|
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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