Organism : Methanococcus maripaludis S2 | Module List :
Regulation information for MMP0939(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 MMP0939
Module neighborhood information for MMP0939
|Gene||Common Name||Description||Module membership|
|Antisense_21||None||37, 119, 151|
|MMP0001||hypothetical protein MMP0001||46, 106, 121, 144|
|MMP0002||L-seryl-tRNA selenium transferase||12, 46, 76, 106, 121|
|MMP0009||putative DNA primase large subunit||75, 151|
|MMP0063||argB||acetylglutamate kinase||49, 151|
|MMP0090||glycosyl transferase||69, 110, 151|
|MMP0176||cell division protein CDC48||1, 46|
|MMP0234||hypothetical protein MMP0234||46, 160|
|MMP0251||psmA||proteasome subunit alpha||46, 68|
|MMP0252||hypothetical protein MMP0252||15, 46|
|MMP0363||methanol dehydrogenase regulatory protein-like protein||15, 46|
|MMP0369||hypothetical protein MMP0369||58, 151|
|MMP0373||hypothetical protein MMP0373||46, 50|
|MMP0374||hypothetical protein MMP0374||15, 46|
|MMP0387||microsomal signal peptidase 21 KD subunit||46, 50|
|MMP0394||hemD||uroporphyrinogen III synthase||15, 46|
|MMP0395||hypothetical protein MMP0395||15, 46|
|MMP0411||comD||sulfopyruvate decarboxylase subunit alpha||15, 46|
|MMP0427||rfc||replication factor C small subunit||12, 46|
|MMP0475||hypothetical protein MMP0475||26, 31, 45, 72, 82, 151|
|MMP0515||modB||molybdenum ABC transporter permease||6, 53, 72, 110, 151|
|MMP0516||modD||quinolinate phosphoribosyl transferase||46, 68|
|MMP0585||UspA domain-containing protein||83, 151, 152|
|MMP0598||phosphoglycerate mutase-related||106, 151|
|MMP0614||iron-sulfur flavoprotein||43, 125, 151|
|MMP0656||hypothetical protein MMP0656||46, 160|
|MMP0658||MoaA/nifB/pqqE family protein||46, 90|
|MMP0725||putative integral membrane protein||49, 75, 90, 151|
|MMP0729||uvrA||excinuclease ABC subunit A||46, 90|
|MMP0769||hypothetical protein MMP0769||36, 53, 151, 161|
|MMP0886||cobalt ABC transporter inner membrane protein||4, 151|
|MMP0939||HAD superfamily (subfamily IA) hydrolase||46, 151|
|MMP1056||hypothetical protein MMP1056||119, 151|
|MMP1168||ABC transporter ATP-binding protein||15, 46|
|MMP1169||SufBD protein||15, 46|
|MMP1179||methyltransferase||85, 110, 151|
|MMP1185||hydrogen uptake protein:hydrogenase maturation protease HycI||1, 46|
|MMP1197||binding-protein dependent transport system inner membrane protein||12, 46|
|MMP1217||hypothetical protein MMP1217||12, 46|
|MMP1218||hypothetical protein MMP1218||12, 46, 49|
|MMP1221||SAM-binding motif-containing protein||46, 83|
|MMP1262||hypothetical protein MMP1262||14, 151|
|MMP1343||hypothetical protein MMP1343||49, 151|
|MMP1388||redox-active disulfide protein 2||99, 151|
|MMP1390||hypothetical protein MMP1390||46, 99|
|MMP1477||cbiA||cobyrinic acid a,c-diamide synthase||46, 152|
|MMP1525||modulator of DNA gyrase||100, 151|
|MMP1526||rncS||ribonuclease III family protein||36, 53, 151|
|MMP1679||hypothetical protein MMP1679||117, 151|
|RNA_23||tRNA-Glu2||Glu tRNA||88, 100, 101, 151, 165|
|RNA_47||rrnB5S||5S ribosomal RNA||100, 101, 151|
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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