Organism : Methanococcus maripaludis S2 | Module List :
Regulation information for MMP0707(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 MMP0707
Module neighborhood information for MMP0707
|Gene||Common Name||Description||Module membership|
|MMP0033||LysR family protein||87, 109|
|MMP0036||tfe||transcription initiation factor E subunit alpha||49, 87, 92, 129|
|MMP0046||hypothetical protein MMP0046||20, 51, 140|
|MMP0074||hypothetical protein MMP0074||51, 140|
|MMP0092||rpoF||DNA-directed RNA polymerase subunit F||87, 109|
|MMP0106||hypothetical protein MMP0106||107, 140|
|MMP0133||guaB||inosine-5'-monophosphate dehydrogenase||25, 120, 140|
|MMP0155||hypothetical protein MMP0155||61, 87|
|MMP0210||hypothetical protein MMP0210||58, 140|
|MMP0220||Sodium/proline symporter-related||70, 140|
|MMP0224||hemL||glutamate-1-semialdehyde aminotransferase||60, 130, 140|
|MMP0246||hypothetical protein MMP0246||87, 109|
|MMP0247||ribosomal biogenesis protein||87, 109|
|MMP0248||DNA-directed RNA polymerase-like protein||87, 109|
|MMP0282||purE||phosphoribosylaminoimidazole carboxylase catalytic subunit||7, 140|
|MMP0316||iorA1||indolepyruvate oxidoreductase subunit alpha 1||25, 64, 87|
|MMP0319||cbiL||precorrin-2 C-20 methyltransferase||24, 140, 141, 149|
|MMP0346||2-hydroxyglutaryl-CoA dehydratase subunit D-like protein||7, 140|
|MMP0356||group 1 glycosyl transferase||80, 139, 140|
|MMP0384||hypothetical protein MMP0384||61, 87|
|MMP0398||hypothetical protein MMP0398||70, 80, 87|
|MMP0403||hypothetical protein MMP0403||87, 115|
|MMP0404||cofD||2-phospho-L-lactate transferase||87, 137|
|MMP0412||MiaB-like tRNA modifying protein||4, 25, 87|
|MMP0530||hypothetical protein MMP0530||92, 140|
|MMP0531||hypothetical protein MMP0531||106, 140|
|MMP0541||serB||phosphoserine phosphatase SerB||7, 40, 139, 140|
|MMP0550||amino acid ABC transporter periplasmic protein||81, 140|
|MMP0554||SAM-binding motif-containing protein||129, 140|
|MMP0566||AMP-binding domain-containing protein||92, 109|
|MMP0568||transcriptional regulator-like protein||109, 162|
|MMP0588||dph5||diphthine synthase||25, 81, 140|
|MMP0603||aIF-1A||translation initiation factor IF-1A||29, 87, 109, 162|
|MMP0604||hypothetical protein MMP0604||87, 109|
|MMP0609||pth2||peptidyl-tRNA hydrolase||66, 140|
|MMP0671||ywbE||hypothetical protein MMP0671||51, 87|
|MMP0694||beta-lactamase-like protein||51, 109, 149|
|MMP0705||wbpI||UDP-N-acetylglucosamine 2-epimerase||80, 140|
|MMP0707||sodium/hydrogen exchanger||87, 109, 140|
|MMP0865||aminotransferase (subgroup II) adenosylmethionine-8-amino-7-oxononanoate aminotransferase||115, 140|
|MMP0878||ribonuclease P-like protein||25, 87, 140|
|MMP0880||aksF||isopropylmalate/isohomocitrate dehydrogenase||24, 60, 140, 143|
|MMP0999||hypothetical protein MMP0999||95, 140|
|MMP1068||K+-dependent Na+/Ca+ exchanger related-protein:Sodium/calcium exchanger membrane region||81, 140|
|MMP1106||hypothetical protein MMP1106||81, 137, 140|
|MMP1114||rpe||Pentose-5-phosphate 3-epimerase||109, 120|
|MMP1115||transketolase, N terminal half||109, 120|
|MMP1312||hypothetical protein MMP1312||52, 140|
|MMP1326||rpoN||DNA-directed RNA polymerase subunit N||103, 118, 140|
|MMP1353||hypothetical protein MMP1353||81, 140|
|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|
|MMP1362||rpoB1||DNA-directed RNA polymerase subunit B'||63, 130, 140|
|MMP1425||tRNA 2'-O-methylase||25, 87, 140|
|MMP1426||dcd||bifunctional dCTP deaminase/dUTP diphosphatase||16, 112, 140|
|MMP1438||hypothetical protein MMP1438||14, 140|
|MMP1480||aconitase family||60, 87, 92|
|MMP1540||hypothetical protein MMP1540||24, 140|
|MMP1582||pdaD||pyruvoyl-dependent arginine decarboxylase||87, 149|
|MMP1710||hypothetical protein MMP1710||20, 87, 92|
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
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