Organism : Methanococcus maripaludis S2 | Module List :
hypothetical protein MMP1001
Functional Annotations (1)
|Uncharacterized conserved protein||cog/ cog|
Regulation information for MMP1001(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 MMP1001
|Uncharacterized conserved protein||cog/ cog|
Module neighborhood information for MMP1001
|Gene||Common Name||Description||Module membership|
|MMP0001||hypothetical protein MMP0001||46, 106, 121, 144|
|MMP0002||L-seryl-tRNA selenium transferase||12, 46, 76, 106, 121|
|MMP0027||TrkA-N domain-containing protein||54, 57|
|MMP0030||MCM family DNA replication protein||106, 117|
|MMP0084||hypothetical protein MMP0084||49, 106|
|MMP0085||hypothetical protein MMP0085||22, 106|
|MMP0091||hypothetical protein MMP0091||51, 106|
|MMP0121||hypothetical protein MMP0121||55, 57|
|MMP0122||hypothetical protein MMP0122||57, 102, 146|
|MMP0207||modC||molybdenum ABC transporter ATP-binding protein||57, 153|
|MMP0239||hypothetical protein MMP0239||1, 49, 75, 106|
|MMP0420||CBS domain-containing protein||13, 106|
|MMP0425||hypothetical protein MMP0425||57, 102, 106|
|MMP0426||nitroreductase family protein||57, 102, 106, 153|
|MMP0465||hypothetical protein MMP0465||57, 102|
|MMP0531||hypothetical protein MMP0531||106, 140|
|MMP0534||mechanosensitive ion channel MscS||57, 102|
|MMP0535||hypothetical protein MMP0535||57, 102, 106|
|MMP0569||hypothetical protein MMP0569||57, 102|
|MMP0598||phosphoglycerate mutase-related||106, 151|
|MMP0605||putative RNA-processing protein||12, 106|
|MMP0612||LigT||2'-5' RNA ligase||54, 57|
|MMP0621||xylose isomerase domain-containing protein||54, 57|
|MMP0630||feoB||ferrous iron transporter||28, 76, 106, 121|
|MMP0808||hypothetical protein MMP0808||12, 106|
|MMP0809||phosphoribosylaminoimidazole carboxylase-like protein||12, 106|
|MMP0958||hypothetical protein MMP0958||57, 102, 106|
|MMP0959||trxB||FAD-dependent pyridine nucleotide-disulfide oxidoreductase||57, 102, 106|
|MMP0969||hypothetical protein MMP0969||106, 115|
|MMP1001||hypothetical protein MMP1001||57, 102, 106|
|MMP1051||surE||stationary phase survival protein SurE||12, 28, 106|
|MMP1052||hypothetical protein MMP1052||12, 102|
|MMP1060||cysS||cysteinyl-tRNA synthetase||33, 102|
|MMP1069||basic helix-loop-helix dimerization domain-containing protein||106, 115|
|MMP1071||hypothetical protein MMP1071||1, 106|
|MMP1072||aminotransferase (subgroup I) aromatic aminotransferase||1, 106|
|MMP1073||ehbC||putative monovalent cation/H+ antiporter subunit G||35, 106|
|MMP1074||ehbD||hypothetical protein MMP1074||17, 106|
|MMP1091||ADP-glucose pyrophosphorylase||99, 106|
|MMP1124||thiamine-monophosphate kinase||102, 146|
|MMP1234||UBA/THIF-type NAD/FAD binding protein||33, 54, 55, 106|
|MMP1235||moaE||molybdopterin biosynthesis MoaE||49, 55, 106, 117, 150|
|MMP1282||hypothetical protein MMP1282||49, 102, 106, 150|
|MMP1283||hypothetical protein MMP1283||49, 102, 150|
|MMP1469||ehbA||putative monovalent cation/H+ antiporter subunit E||10, 106|
|MMP1514||tyrA||prephenate dehydrogenase||57, 102|
|MMP1573||bioD||dethiobiotin synthase||28, 106|
|MMP1598||hypothetical protein MMP1598||76, 102, 106|
|MMP1611||hypothetical protein MMP1611||21, 106|
|MMP1641||soluble P-type ATPase||54, 57|
|MMP1682||recJ||single stranded DNA-specific exonuclease||21, 106|
|MMP1712||LysR family transcriptional regulator||19, 106|
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.
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