Organism : Methanococcus maripaludis S2
| Module List :
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Regulation information for MMP1241
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
MMP0527 MMP1210 |
117 | combiner |
MMP0568 | 117 | tf |
MMP1065 | 117 | tf |
MMP1065 MMP1210 |
117 | combiner |
MMP0032 MMP0257 |
1 | combiner |
MMP0209 | 1 | tf |
MMP1447 | 1 | tf |
MMP0033 | 94 | tf |
MMP0257 MMP1447 |
94 | combiner |
MMP0568 | 94 | tf |
MMP1065 | 94 | tf |
MMP1447 | 94 | tf |
MMP0460 | 55 | tf |
MMP0527 | 55 | tf |
MMP0907 MMP1023 |
55 | combiner |
MMP0907 MMP1646 |
55 | combiner |
MMP1023 | 55 | tf |
MMP1447 | 55 | tf |
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Motif information (de novo identified motifs for modules)
There are 8 motifs predicted.
Motif Id | e-value | Consensus | Motif Logo |
---|---|---|---|
663 | 3.00e+01 | CgacCC.c.agG |
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664 | 7.60e+03 | CcgcTg |
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771 | 2.40e+01 | gcgatgggg.ggAagA.taCctg |
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772 | 1.60e+03 | AatTGgTGAa |
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845 | 2.00e-02 | tagaTaaaGcgGgaagAa |
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846 | 4.80e+01 | AtcGTTcTagaTAtTtcatAc |
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889 | 2.10e+01 | TTTcttctagaaTATcccgGgtGA |
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890 | 3.40e+01 | TTTTCcagatTttg |
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Module neighborhood information for MMP1241
Gene | Common Name | Description | Module membership |
---|---|---|---|
Antisense_2 | None | 1, 22 | |
Antisense_23 | None | 1, 117 | |
Antisense_5 | None | 1, 22 | |
MMP0030 | MCM family DNA replication protein | 106, 117 | |
MMP0052 | putative CBS domain-containing signal transduction protein | 13, 117 | |
MMP0117 | hypothetical protein MMP0117 | 94, 145 | |
MMP0119 | birA | biotin--acetyl-CoA-carboxylase ligase | 1, 75, 142 |
MMP0120 | hypothetical protein MMP0120 | 55, 142 | |
MMP0121 | hypothetical protein MMP0121 | 55, 57 | |
MMP0153 | aksA | trans-homoaconitate synthase | 1, 143 |
MMP0154 | hypothetical protein MMP0154 | 1, 13 | |
MMP0166 | MATE family drug/sodium antiporter | 1, 28 | |
MMP0167 | ABC transporter ATP-binding protein | 1, 28 | |
MMP0168 | ParR family transcriptional regulator | 1, 28 | |
MMP0176 | cell division protein CDC48 | 1, 46 | |
MMP0177 | hypothetical protein MMP0177 | 83, 117, 152 | |
MMP0180 | ribC | riboflavin synthase | 1, 58 |
MMP0225 | gldA | glycerol dehydrogenase | 117, 142 |
MMP0226 | ExsB family transcriptional regulator | 13, 117 | |
MMP0239 | hypothetical protein MMP0239 | 1, 49, 75, 106 | |
MMP0276 | hypothetical protein MMP0276 | 65, 94 | |
MMP0289 | hypD | hydrogenase expression/formation protein HypD | 12, 117 |
MMP0312 | hypothetical protein MMP0312 | 73, 94 | |
MMP0327 | deoA | thymidine phosphorylase | 94, 152 |
MMP0336 | hjc | Holliday junction resolvase | 13, 94 |
MMP0337 | hypothetical protein MMP0337 | 13, 94 | |
MMP0431 | rhodopsin-like GPCR superfamily protein | 94, 145 | |
MMP0432 | TatD-like deoxyribonuclease | 94, 145 | |
MMP0433 | putative flavodoxin | 94, 145 | |
MMP0439 | pyrD | dihydroorotate dehydrogenase 1B | 117, 119 |
MMP0450 | ferredoxin | 1, 70 | |
MMP0451 | hypothetical protein MMP0451 | 1, 70 | |
MMP0482 | hypothetical protein MMP0482 | 54, 55 | |
MMP0483 | hypothetical protein MMP0483 | 54, 55 | |
MMP0536 | hypothetical protein MMP0536 | 1, 28 | |
MMP0543 | hypothetical protein MMP0543 | 55, 159 | |
MMP0544 | MoaA/nifB/pqqE family protein | 55, 142 | |
MMP0545 | putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein | 55, 142 | |
MMP0548 | hisB | imidazoleglycerol-phosphate dehydratase | 94, 145 |
MMP0549 | hypothetical protein MMP0549 | 94, 145 | |
MMP0608 | 2-hydroxyglutaryl-CoA dehydratase subunit A-like protein | 1, 28 | |
MMP0638 | hypothetical protein MMP0638 | 54, 55 | |
MMP0660 | apt | adenine phosphoribosyltransferase | 83, 94, 152 |
MMP0677 | hypothetical protein MMP0677 | 94, 145 | |
MMP0685 | N-6 adenine-specific DNA methylase | 1, 144 | |
MMP0788 | hypothetical protein MMP0788 | 58, 117 | |
MMP0849 | L-lysine/ homoserine-homoserine lactone exporter family protein | 95, 117 | |
MMP0876 | cofG | FO synthase subunit 1 | 1, 129 |
MMP0902 | hypothetical protein MMP0902 | 12, 49, 55 | |
MMP0903 | hypothetical protein MMP0903 | 33, 54, 55 | |
MMP0992 | hypothetical protein MMP0992 | 55, 117 | |
MMP1065 | BadM/Rrf2 family transcriptional regulator | 55, 152 | |
MMP1071 | hypothetical protein MMP1071 | 1, 106 | |
MMP1072 | aminotransferase (subgroup I) aromatic aminotransferase | 1, 106 | |
MMP1088 | group 1 glycosyl transferase | 31, 117 | |
MMP1118 | hypothetical protein MMP1118 | 83, 117 | |
MMP1140 | fdxA | ferredoxin | 1, 46 |
MMP1145 | minD | septum formation inhibitor-activating ATPase | 94, 145 |
MMP1185 | hydrogen uptake protein:hydrogenase maturation protease HycI | 1, 46 | |
MMP1234 | UBA/THIF-type NAD/FAD binding protein | 33, 54, 55, 106 | |
MMP1235 | moaE | molybdopterin biosynthesis MoaE | 49, 55, 106, 117, 150 |
MMP1236 | hypothetical protein MMP1236 | 22, 55, 117, 142, 152 | |
MMP1238 | bioB | biotin synthase | 1, 153 |
MMP1240 | Sep-tRNA:Cys-tRNA synthetase | 1, 55 | |
MMP1241 | hypothetical protein MMP1241 | 1, 55, 94, 117 | |
MMP1330 | hydrogenase assembly chaperone hypC/hupF | 100, 117 | |
MMP1372 | manB | phosphomannomutase | 49, 94, 152 |
MMP1428 | hypothetical protein MMP1428 | 55, 83 | |
MMP1447 | Cro repressor family protein | 22, 117 | |
MMP1452 | ehaE | hypothetical protein MMP1452 | 22, 117 |
MMP1453 | ehaF | hypothetical protein MMP1453 | 22, 117 |
MMP1454 | ehaG | hypothetical protein MMP1454 | 66, 117, 133 |
MMP1456 | ehaI | hypothetical protein MMP1456 | 66, 117, 133 |
MMP1459 | ehaL | hypothetical protein MMP1459 | 66, 117, 133 |
MMP1461 | ehaN | energy conserving hydrogenase A small subunit | 117, 133 |
MMP1487 | gapN | aldehyde dehydrogenase | 55, 152 |
MMP1548 | Fe-S type hydro-lyase tartrate/fumarate subunit beta | 94, 145 | |
MMP1549 | AP endonuclease | 1, 94, 152 | |
MMP1550 | NADP oxidoreductase, coenzyme F420-dependent | 1, 58 | |
MMP1551 | ffh | signal recognition particle protein Srp54 | 49, 55, 83 |
MMP1605 | pyruvate kinase | 1, 54, 146, 166 | |
MMP1606 | flavoprotein:DNA/pantothenate metabolism flavoprotein | 1, 13, 49 | |
MMP1607 | hypothetical protein MMP1607 | 49, 55, 83 | |
MMP1619 | molybdenum cofactor biosynthesis protein MoeA | 117, 152 | |
MMP1662 | cbiF | precorrin-4 C11-methyltransferase | 66, 117 |
MMP1665 | HEAT domain-containing protein | 66, 117 | |
MMP1679 | hypothetical protein MMP1679 | 117, 151 | |
Unanno_49 | None | 95, 117 |
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.