Organism : Methanococcus maripaludis S2 | Module List :
MiaB-like tRNA modifying protein
Functional Annotations (5)
|2-methylthioadenine synthetase||cog/ cog|
|metabolic process||go/ biological_process|
|2-alkenal reductase [NAD(P)] activity||go/ molecular_function|
|iron-sulfur cluster binding||go/ molecular_function|
Regulation information for MMP0412(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 MMP0412
Module neighborhood information for MMP0412
|Gene||Common Name||Description||Module membership|
|MMP0011||DNA-cytosine methyltransferase||4, 104|
|MMP0026||DP2||DNA polymerase II large subunit||25, 41, 92|
|MMP0033||LysR family protein||87, 109|
|MMP0036||tfe||transcription initiation factor E subunit alpha||49, 87, 92, 129|
|MMP0092||rpoF||DNA-directed RNA polymerase subunit F||87, 109|
|MMP0105||hypothetical protein MMP0105||4, 107|
|MMP0133||guaB||inosine-5'-monophosphate dehydrogenase||25, 120, 140|
|MMP0137||dys||putative deoxyhypusine synthase||25, 141, 149|
|MMP0140||(NiFe) hydrogenase maturation protein HypF||4, 85|
|MMP0155||hypothetical protein MMP0155||61, 87|
|MMP0181||hypothetical protein MMP0181||4, 58|
|MMP0216||cation transport ATPase||4, 41, 95|
|MMP0243||hypothetical protein MMP0243||4, 25, 38|
|MMP0246||hypothetical protein MMP0246||87, 109|
|MMP0247||ribosomal biogenesis protein||87, 109|
|MMP0248||DNA-directed RNA polymerase-like protein||87, 109|
|MMP0284||infB||translation initiation factor IF-2||25, 149|
|MMP0296||hypothetical protein MMP0296||4, 129|
|MMP0315||iorB1||indolepyruvate oxidoreductase subunit B||25, 64|
|MMP0316||iorA1||indolepyruvate oxidoreductase subunit alpha 1||25, 64, 87|
|MMP0333||hypothetical protein MMP0333||4, 126|
|MMP0384||hypothetical protein MMP0384||61, 87|
|MMP0392||purD||phosphoribosylamine--glycine ligase||4, 75, 104|
|MMP0398||hypothetical protein MMP0398||70, 80, 87|
|MMP0401||metE||methionine synthase||4, 15, 80|
|MMP0403||hypothetical protein MMP0403||87, 115|
|MMP0404||cofD||2-phospho-L-lactate transferase||87, 137|
|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|
|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|
|MMP0610||tgtA||7-cyano-7-deazaguanine tRNA-ribosyltransferase||25, 41|
|MMP0671||ywbE||hypothetical protein MMP0671||51, 87|
|MMP0707||sodium/hydrogen exchanger||87, 109, 140|
|MMP0878||ribonuclease P-like protein||25, 87, 140|
|MMP0886||cobalt ABC transporter inner membrane protein||4, 151|
|MMP0921||RNAse P, Rpr2/Rpp21 subunit||25, 141|
|MMP0948||hypothetical protein MMP0948||4, 115|
|MMP0949||tRNA CCA-pyrophosphorylase||4, 70|
|MMP0953||cbiH||precorrin-3B C17-methyltransferase||24, 25, 149|
|MMP1000||hypothetical protein MMP1000||4, 95|
|MMP1011||gltX||glutamyl-tRNA synthetase||25, 129|
|MMP1014||radical SAM domain-containing protein||25, 141|
|MMP1048||hypothetical protein MMP1048||14, 25|
|MMP1064||adenylate cyclase||4, 51|
|MMP1130||hypothetical protein MMP1130||4, 38|
|MMP1150||mtaA||uroporphyrinogen decarboxylase||4, 41, 95|
|MMP1195||yneG||putative cytoplasmic protein||25, 126|
|MMP1228||hypothetical protein MMP1228||4, 22, 142|
|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|
|MMP1356||PP-loop domain-containing protein||25, 129, 139, 140, 149|
|MMP1361||rpoB2||DNA-directed RNA polymerase subunit beta''||25, 92, 109, 149|
|MMP1425||tRNA 2'-O-methylase||25, 87, 140|
|MMP1480||aconitase family||60, 87, 92|
|MMP1582||pdaD||pyruvoyl-dependent arginine decarboxylase||87, 149|
|MMP1645||aspartate/glutamate/uridylate kinase||4, 126|
|MMP1698||hypothetical protein MMP1698||4, 8|
|MMP1710||hypothetical protein MMP1710||20, 87, 92|
|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.
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
- 3. Target genes (other module members)
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