Organism : Methanococcus maripaludis S2 | Module List :
hypothetical protein MMP1264
Functional Annotations (1)
|Predicted ATPase||cog/ cog|
Regulation information for MMP1264(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 MMP1264
|Predicted ATPase||cog/ cog|
Module neighborhood information for MMP1264
|Gene||Common Name||Description||Module membership|
|MMP0008||DP1||DNA polymerase II small subunit||22, 75, 142|
|MMP0011||DNA-cytosine methyltransferase||4, 104|
|MMP0017||hypothetical protein MMP0017||67, 142|
|MMP0019||hypothetical protein MMP0019||14, 104, 142|
|MMP0021||hypothetical protein MMP0021||14, 142|
|MMP0077||radical SAM domain-containing protein||35, 104|
|MMP0113||hypothetical protein MMP0113||23, 75, 142|
|MMP0119||birA||biotin--acetyl-CoA-carboxylase ligase||1, 75, 142|
|MMP0120||hypothetical protein MMP0120||55, 142|
|MMP0125||flpA||fibrillarin-like protein||14, 104|
|MMP0126||bioB||biotin synthase||14, 104|
|MMP0131||L-tyrosine decarboxylase||111, 122, 129, 157|
|MMP0161||comB||2-phosphosulfolactate phosphatase||85, 104|
|MMP0170||cofF||RimK family alpha-L-glutamate ligase||104, 133|
|MMP0185||mtaP||5'-methylthioadenosine phosphorylase||122, 157|
|MMP0186||hypothetical protein MMP0186||104, 133|
|MMP0214||putative deoxyribonucleotide triphosphate pyrophosphatase||12, 104|
|MMP0218||hypothetical protein MMP0218||15, 52, 104|
|MMP0222||hypothetical protein MMP0222||14, 122, 157|
|MMP0225||gldA||glycerol dehydrogenase||117, 142|
|MMP0236||hypothetical protein MMP0236||75, 104|
|MMP0324||hypothetical protein MMP0324||62, 142|
|MMP0328||hypothetical protein MMP0328||15, 157|
|MMP0329||hypothetical protein MMP0329||122, 157|
|MMP0330||cbiC||precorrin-8X methylmutase||68, 122, 157|
|MMP0357||UDP-N-acetylglucosamine 2-epimerase||139, 157|
|MMP0358||hypothetical protein MMP0358||139, 157|
|MMP0379||hypothetical protein MMP0379||104, 163|
|MMP0380||dnaB||DNA polymerase family B protein||15, 104|
|MMP0390||hypothetical protein MMP0390||15, 157|
|MMP0392||purD||phosphoribosylamine--glycine ligase||4, 75, 104|
|MMP0544||MoaA/nifB/pqqE family protein||55, 142|
|MMP0545||putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein||55, 142|
|MMP0706||NAD binding site:UDP-glucose/GDP-mannose dehydrogenase||111, 157|
|MMP0727||uvrB||excinuclease ABC subunit B||49, 142|
|MMP0728||uvrC||excinuclease ABC subunit C||90, 142|
|MMP0731||exodeoxyribonuclease VII small subunit||85, 104|
|MMP0895||hypothetical protein MMP0895||14, 104|
|MMP0909||hypothetical protein MMP0909||75, 104|
|MMP0986||thyA||thymidylate synthase||104, 142|
|MMP1024||MCE family-like protein||14, 47, 157|
|MMP1027||hypothetical protein MMP1027||104, 163|
|MMP1062||hypothetical protein MMP1062||142, 144|
|MMP1080||group 1 glycosyl transferase||14, 142|
|MMP1121||metal-dependent phophohydrolase-like protein||129, 157|
|MMP1132||endA||tRNA-splicing endonuclease subunit alpha||122, 157|
|MMP1133||comC||L-sulfolactate dehydrogenase/(S)-hydroxyglutaric acid dehydrogenase||122, 157|
|MMP1141||ATP-dependent helicase||75, 142|
|MMP1202||hypothetical protein MMP1202||104, 153|
|MMP1203||cbiD||cobalt-precorrin-6A synthase||104, 153|
|MMP1228||hypothetical protein MMP1228||4, 22, 142|
|MMP1232||PP-loop domain-containing protein||95, 104|
|MMP1236||hypothetical protein MMP1236||22, 55, 117, 142, 152|
|MMP1264||hypothetical protein MMP1264||104, 142, 157|
|MMP1344||hypothetical protein MMP1344||111, 157|
|MMP1346||basic helix-loop-helix dimerization domain-containing protein||49, 67, 142|
|MMP1350||radical SAM domain-containing protein||14, 47, 104|
|MMP1377||hypothetical protein MMP1377||69, 104|
|MMP1398||dapE||diaminopimelate aminotransferase||22, 142|
|MMP1485||moaB||molybdenum cofactor biosynthesis protein||104, 142|
|MMP1494||hypothetical protein MMP1494||104, 153|
|MMP1500||ftsz2||cell division protein FtsZ||139, 157|
|MMP1521||hypothetical protein MMP1521||14, 111, 122, 157|
|MMP1597||phosphatidylglycerophosphatase A||22, 142, 144|
|MMP1600||ribosomal protein S6 modification protein||104, 129|
|Unanno_59||None||28, 104, 133|
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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