Organism : Methanococcus maripaludis S2 | Module List :
MMP1085
hypothetical protein MMP1085
Functional Annotations (2)
Function | System |
---|---|
metabolic process | go/ biological_process |
methyltransferase activity | go/ molecular_function |
Regulation information for MMP1085
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
MMP0033 | 149 | tf |
MMP0052 MMP0480 |
149 | combiner |
MMP0607 | 149 | tf |
MMP0637 MMP0678 |
149 | combiner |
MMP1467 MMP1646 |
149 | combiner |
MMP1704 | 149 | tf |
MMP0033 | 141 | tf |
MMP0607 | 141 | tf |
MMP0907 MMP1646 |
141 | combiner |
MMP1704 | 141 | tf |
Motif information (de novo identified motifs for modules)
There are 6 motifs predicted.
Motif Id | e-value | Consensus | Motif Logo |
---|---|---|---|
933 | 7.10e+01 | ATctctAtTcTttacATtcc | |
934 | 6.20e+03 | GCAAATCATATTTGGTTTCATAC | |
937 | 2.40e+03 | GAGcGCCC | |
938 | 4.70e+03 | ccca.CAatTc.gc.AtaT | |
947 | 6.00e-01 | taTTaa.cggtGgt | |
948 | 1.50e+02 | tCTgtcc.tct.gga.gcat |
Functional Enrichment for MMP1085
Function | System |
---|---|
metabolic process | go/ biological_process |
methyltransferase activity | go/ molecular_function |
Module neighborhood information for MMP1085
Gene | Common Name | Description | Module membership |
---|---|---|---|
MMP0007 | geranylgeranylglyceryl phosphate synthase-like protein | 12, 143 | |
MMP0034 | GTP cyclohydrolase | 130, 149 | |
MMP0137 | dys | putative deoxyhypusine synthase | 25, 141, 149 |
MMP0145 | hpt | adenine phosphoribosyltransferase | 137, 143 |
MMP0153 | aksA | trans-homoaconitate synthase | 1, 143 |
MMP0178 | purQ | phosphoribosylformylglycinamidine synthase I | 95, 143 |
MMP0179 | purL | phosphoribosylformylglycinamidine synthase | 66, 143 |
MMP0187 | thiC | thiamine biosynthesis protein ThiC | 137, 143 |
MMP0264 | MscMJ | mechanosensitive ion channel MscS | 129, 143 |
MMP0284 | infB | translation initiation factor IF-2 | 25, 149 |
MMP0319 | cbiL | precorrin-2 C-20 methyltransferase | 24, 140, 141, 149 |
MMP0320 | shikimate kinase | 47, 141 | |
MMP0340 | pycB | pyruvate carboxylase subunit B | 24, 86, 120, 141, 149 |
MMP0415 | O-sialoglycoprotein endopeptidase/protein kinase | 47, 149 | |
MMP0418 | carbohydrate kinase PfkB | 60, 137, 143 | |
MMP0540 | purC | phosphoribosylaminoimidazole-succinocarboxamide synthase | 8, 112, 143 |
MMP0564 | hypothetical protein MMP0564 | 111, 149 | |
MMP0606 | ribosomal RNA methyltransferase RrmJ/FtsJ | 137, 143 | |
MMP0607 | nrpR | hypothetical protein MMP0607 | 115, 137, 143 |
MMP0694 | beta-lactamase-like protein | 51, 109, 149 | |
MMP0697 | leuS | leucyl-tRNA synthetase | 8, 143 |
MMP0698 | hypothetical protein MMP0698 | 21, 143 | |
MMP0879 | serS | seryl-tRNA synthetase | 27, 143 |
MMP0880 | aksF | isopropylmalate/isohomocitrate dehydrogenase | 24, 60, 140, 143 |
MMP0905 | hypothetical protein MMP0905 | 14, 149 | |
MMP0906 | ribonuclease Z | 129, 149 | |
MMP0907 | transcriptional regulator TrmB | 14, 149 | |
MMP0919 | dihydroorotate dehydrogenase electron transfer subunit | 86, 141 | |
MMP0920 | ahcY | S-adenosyl-L-homocysteine hydrolase | 80, 141 |
MMP0921 | RNAse P, Rpr2/Rpp21 subunit | 25, 141 | |
MMP0941 | hypothetical protein MMP0941 | 129, 149 | |
MMP0953 | cbiH | precorrin-3B C17-methyltransferase | 24, 25, 149 |
MMP0989 | top6B | DNA topoisomerase VI subunit B | 139, 141 |
MMP1014 | radical SAM domain-containing protein | 25, 141 | |
MMP1063 | leuA | 2-isopropylmalate synthase | 81, 143 |
MMP1081 | wbpG | putative LPS biosynthesis protein WbpG | 137, 143 |
MMP1082 | hisH | imidazole glycerol phosphate synthase subunit HisH | 66, 143 |
MMP1083 | imidazole glycerol phosphate synthase subunit HisF | 137, 143 | |
MMP1085 | hypothetical protein MMP1085 | 141, 143, 149 | |
MMP1086 | hypothetical protein MMP1086 | 122, 141 | |
MMP1107 | Signal recognition particle protein SRP19 | 111, 141 | |
MMP1108 | corA | magnesium/cobalt transporter CorA | 141, 149 |
MMP1112 | hypothetical protein MMP1112 | 111, 129, 141, 149 | |
MMP1122 | translation-associated GTPase | 137, 143 | |
MMP1146 | purF | amidophosphoribosyltransferase | 7, 60, 137, 143 |
MMP1198 | nitrate/sulfonate/bicarbonate ABC transporter ATPase | 12, 143 | |
MMP1307 | methyltransferase-like protein | 4, 149 | |
MMP1313 | fen-1 | flap endonuclease-1 | 47, 52, 141 |
MMP1327 | rpoK | RNA polymerase Rpb6 | 103, 139, 149 |
MMP1328 | enolase | 103, 139, 149 | |
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 |
MMP1491 | trzA | amidohydrolase | 14, 111, 122, 149 |
MMP1492 | pyrE | orotate phosphoribosyltransferase | 14, 149 |
MMP1496 | pheS | phenylalanyl-tRNA synthetase subunit alpha | 137, 143 |
MMP1582 | pdaD | pyruvoyl-dependent arginine decarboxylase | 87, 149 |
MMP1592 | trpS | tryptophanyl-tRNA synthetase | 27, 143 |
MMP1594 | hypothetical protein MMP1594 | 51, 143 | |
MMP1614 | hisS | histidyl-tRNA synthetase | 141, 149 |
MMP1681 | hypothetical protein MMP1681 | 21, 143 | |
Unanno_24 | None | 95, 143 |
Gene Page Help
Network Tab
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.
Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
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Regulation Tab
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.
Motifs Tab
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.
Functions Tab
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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CircVis
Our 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)
- 4. Interactions between source and target genes for a particular module
- 5. Module(s) that source gene and target genes belong to
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In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.