Organism : Methanococcus maripaludis S2
| Module List :
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MMP0002
L-seryl-tRNA selenium transferase
Functional Annotations (11)
Function | System |
---|---|
Selenocysteine synthase [seryl-tRNASer selenium transferase] | cog/ cog |
selenocysteine incorporation | go/ biological_process |
L-seryl-tRNASec selenium transferase activity | go/ molecular_function |
cytoplasm | go/ cellular_component |
biosynthetic process | go/ biological_process |
transferase activity, transferring nitrogenous groups | go/ molecular_function |
pyridoxal phosphate binding | go/ molecular_function |
Selenocompound metabolism | kegg/ kegg pathway |
Aminoacyl-tRNA biosynthesis | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
pyridox_MJ0158 | tigr/ tigrfam |
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Regulation information for MMP0002
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
MMP0041 MMP1023 |
106 | combiner |
MMP0460 MMP0799 |
106 | combiner |
MMP0568 H2 |
106 | combiner |
MMP0799 MMP1065 |
106 | combiner |
MMP1065 | 106 | tf |
MMP0033 MMP1304 |
46 | combiner |
MMP0086 H2 |
46 | combiner |
MMP0460 H2 |
46 | combiner |
MMP0465 MMP0637 |
46 | combiner |
MMP0568 MMP1304 |
46 | combiner |
MMP0607 MMP1304 |
46 | combiner |
MMP1023 MMP1303 |
46 | combiner |
MMP1304 H2 |
46 | combiner |
MMP1304 MMP1704 |
46 | combiner |
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Motif information (de novo identified motifs for modules)
There are 10 motifs predicted.
Motif Id | e-value | Consensus | Motif Logo |
---|---|---|---|
685 | 2.80e+02 | cggcatTTTAtaAatCTAtaTgA |
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686 | 1.60e+03 | cgCTaGATtTTgATTGaTGCc |
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753 | 8.00e+02 | AtCACC |
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754 | 1.10e+03 | Tcagg.aGGatgGtG |
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813 | 4.40e+02 | CAGtTtTTcc |
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814 | 6.80e+03 | cGGGCA |
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869 | 1.10e+03 | CGAGTAAACCGGATAGCTTAC |
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870 | 5.60e+03 | TGaagGGCaGtggcA |
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895 | 1.60e+01 | gtt.ggTg.TcAt.tgGcAaatc |
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896 | 2.00e+02 | CCAGGGTCTTTGAGC |
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Functional Enrichment for MMP0002
Function | System |
---|---|
Selenocysteine synthase [seryl-tRNASer selenium transferase] | cog/ cog |
selenocysteine incorporation | go/ biological_process |
L-seryl-tRNASec selenium transferase activity | go/ molecular_function |
cytoplasm | go/ cellular_component |
biosynthetic process | go/ biological_process |
transferase activity, transferring nitrogenous groups | go/ molecular_function |
pyridoxal phosphate binding | go/ molecular_function |
Selenocompound metabolism | kegg/ kegg pathway |
Aminoacyl-tRNA biosynthesis | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
pyridox_MJ0158 | tigr/ tigrfam |
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Module neighborhood information for MMP0002
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 | |
MMP0007 | geranylgeranylglyceryl phosphate synthase-like protein | 12, 143 | |
MMP0030 | MCM family DNA replication protein | 106, 117 | |
MMP0054 | hypothetical protein MMP0054 | 76, 121 | |
MMP0055 | putative RNA-binding protein | 76, 121 | |
MMP0078 | hypothetical protein MMP0078 | 12, 111 | |
MMP0079 | orotate phosphoribosyltransferase-like protein | 12, 111 | |
MMP0084 | hypothetical protein MMP0084 | 49, 106 | |
MMP0085 | hypothetical protein MMP0085 | 22, 106 | |
MMP0091 | hypothetical protein MMP0091 | 51, 106 | |
MMP0176 | cell division protein CDC48 | 1, 46 | |
MMP0214 | putative deoxyribonucleotide triphosphate pyrophosphatase | 12, 104 | |
MMP0234 | hypothetical protein MMP0234 | 46, 160 | |
MMP0239 | hypothetical protein MMP0239 | 1, 49, 75, 106 | |
MMP0251 | psmA | proteasome subunit alpha | 46, 68 |
MMP0252 | hypothetical protein MMP0252 | 15, 46 | |
MMP0269 | hypothetical protein MMP0269 | 76, 152 | |
MMP0289 | hypD | hydrogenase expression/formation protein HypD | 12, 117 |
MMP0363 | methanol dehydrogenase regulatory protein-like protein | 15, 46 | |
MMP0373 | hypothetical protein MMP0373 | 46, 50 | |
MMP0374 | hypothetical protein MMP0374 | 15, 46 | |
MMP0387 | microsomal signal peptidase 21 KD subunit | 46, 50 | |
MMP0394 | hemD | uroporphyrinogen III synthase | 15, 46 |
MMP0395 | hypothetical protein MMP0395 | 15, 46 | |
MMP0411 | comD | sulfopyruvate decarboxylase subunit alpha | 15, 46 |
MMP0420 | CBS domain-containing protein | 13, 106 | |
MMP0425 | hypothetical protein MMP0425 | 57, 102, 106 | |
MMP0426 | nitroreductase family protein | 57, 102, 106, 153 | |
MMP0427 | rfc | replication factor C small subunit | 12, 46 |
MMP0516 | modD | quinolinate phosphoribosyl transferase | 46, 68 |
MMP0527 | hypothetical protein MMP0527 | 76, 153 | |
MMP0531 | hypothetical protein MMP0531 | 106, 140 | |
MMP0535 | hypothetical protein MMP0535 | 57, 102, 106 | |
MMP0598 | phosphoglycerate mutase-related | 106, 151 | |
MMP0602 | pyrF | orotidine-5'-phosphate decarboxylase | 12, 111 |
MMP0605 | putative RNA-processing protein | 12, 106 | |
MMP0630 | feoB | ferrous iron transporter | 28, 76, 106, 121 |
MMP0631 | putative iron dependent repressor | 28, 121, 144 | |
MMP0656 | hypothetical protein MMP0656 | 46, 160 | |
MMP0658 | MoaA/nifB/pqqE family protein | 46, 90 | |
MMP0678 | hypothetical protein MMP0678 | 73, 76 | |
MMP0684 | hsp20 | heat shock protein Hsp20 | 28, 121 |
MMP0686 | fructose-bisphosphate aldolase | 13, 121 | |
MMP0729 | uvrA | excinuclease ABC subunit A | 46, 90 |
MMP0787 | MarR family transcriptional regulator | 12, 121 | |
MMP0808 | hypothetical protein MMP0808 | 12, 106 | |
MMP0809 | phosphoribosylaminoimidazole carboxylase-like protein | 12, 106 | |
MMP0812 | hypothetical protein MMP0812 | 12, 28 | |
MMP0885 | ATP/GTP-binding motif-containing protein | 76, 121 | |
MMP0902 | hypothetical protein MMP0902 | 12, 49, 55 | |
MMP0939 | HAD superfamily (subfamily IA) hydrolase | 46, 151 | |
MMP0958 | hypothetical protein MMP0958 | 57, 102, 106 | |
MMP0959 | trxB | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | 57, 102, 106 |
MMP0969 | hypothetical protein MMP0969 | 106, 115 | |
MMP0995 | hypothetical protein MMP0995 | 76, 144 | |
MMP1001 | hypothetical protein MMP1001 | 57, 102, 106 | |
MMP1002 | trpA | tryptophan synthase subunit alpha | 76, 121 |
MMP1003 | trpB | tryptophan synthase subunit beta | 76, 121 |
MMP1004 | trpF | N-(5'-phosphoribosyl)anthranilate isomerase | 76, 121 |
MMP1005 | trpG | anthranilate synthase component II | 76, 121 |
MMP1006 | trpE | anthranilate synthase component I | 76, 121 |
MMP1007 | trpD | anthranilate phosphoribosyltransferase | 76, 121 |
MMP1008 | trpC | indole-3-glycerol-phosphate synthase | 76, 121 |
MMP1026 | argS | arginyl-tRNA synthetase | 12, 21 |
MMP1049 | multiple resistance and pH regulation protein F | 12, 99 | |
MMP1051 | surE | stationary phase survival protein SurE | 12, 28, 106 |
MMP1052 | hypothetical protein MMP1052 | 12, 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 | |
MMP1140 | fdxA | ferredoxin | 1, 46 |
MMP1168 | ABC transporter ATP-binding protein | 15, 46 | |
MMP1169 | SufBD protein | 15, 46 | |
MMP1185 | hydrogen uptake protein:hydrogenase maturation protease HycI | 1, 46 | |
MMP1197 | binding-protein dependent transport system inner membrane protein | 12, 46 | |
MMP1198 | nitrate/sulfonate/bicarbonate ABC transporter ATPase | 12, 143 | |
MMP1217 | hypothetical protein MMP1217 | 12, 46 | |
MMP1218 | hypothetical protein MMP1218 | 12, 46, 49 | |
MMP1221 | SAM-binding motif-containing protein | 46, 83 | |
MMP1234 | UBA/THIF-type NAD/FAD binding protein | 33, 54, 55, 106 | |
MMP1235 | moaE | molybdopterin biosynthesis MoaE | 49, 55, 106, 117, 150 |
MMP1259 | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | 12, 21 | |
MMP1282 | hypothetical protein MMP1282 | 49, 102, 106, 150 | |
MMP1390 | hypothetical protein MMP1390 | 46, 99 | |
MMP1469 | ehbA | putative monovalent cation/H+ antiporter subunit E | 10, 106 |
MMP1477 | cbiA | cobyrinic acid a,c-diamide synthase | 46, 152 |
MMP1573 | bioD | dethiobiotin synthase | 28, 106 |
MMP1576 | hypothetical protein MMP1576 | 12, 99 | |
MMP1598 | hypothetical protein MMP1598 | 76, 102, 106 | |
MMP1599 | trkA | TrkA-N domain-containing protein | 76, 121 |
MMP1603 | ferredoxin | 12, 49 | |
MMP1611 | hypothetical protein MMP1611 | 21, 106 | |
MMP1682 | recJ | single stranded DNA-specific exonuclease | 21, 106 |
MMP1712 | LysR family transcriptional regulator | 19, 106 | |
Unanno_36 | None | 46, 121 | |
Unanno_55 | None | 76, 121 | |
Unanno_7 | None | 23, 46 |
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.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.
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.
Help Tab
This help page. More general help can be accessed by clicking help menu in the main navigation bar.
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;![](/static/images/help_images/circvis-help.png)
- 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
- 6. Visualisation legend
Social Tab
Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.
Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.
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.