Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3347

methionine synthase, 5-methyltetrahydrofolate--homocysteine methyltransferase (NCBI)

CircVis
Functional Annotations (10)
Function System
Methionine synthase I (cobalamin-dependent), methyltransferase domain cog/ cog
methionine synthase activity go/ molecular_function
homocysteine S-methyltransferase activity go/ molecular_function
methionine biosynthetic process go/ biological_process
cobalamin binding go/ molecular_function
cobalt ion binding go/ molecular_function
Cysteine and methionine metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3347
(Mouseover regulator name to see its description)

RSP_3347 is regulated by 36 influences and regulates 0 modules.
Regulators for RSP_3347 (36)
Regulator Module Operator
RSP_0443 135 tf
RSP_0547 135 tf
RSP_1014 135 tf
RSP_1663 135 tf
RSP_1712 135 tf
RSP_1866 135 tf
RSP_1890 135 tf
RSP_1990 135 tf
RSP_2200 135 tf
RSP_2324 135 tf
RSP_2362 135 tf
RSP_2780 135 tf
RSP_2800 135 tf
RSP_2889 135 tf
RSP_2950 135 tf
RSP_3238 135 tf
RSP_0386 32 tf
RSP_0623 32 tf
RSP_1014 32 tf
RSP_1055 32 tf
RSP_1139 32 tf
RSP_1163 32 tf
RSP_1164 32 tf
RSP_1606 32 tf
RSP_1712 32 tf
RSP_1739 32 tf
RSP_1945 32 tf
RSP_2130 32 tf
RSP_2324 32 tf
RSP_2362 32 tf
RSP_2572 32 tf
RSP_2950 32 tf
RSP_2963 32 tf
RSP_3165 32 tf
RSP_3238 32 tf
RSP_3620 32 tf

Warning: RSP_3347 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
7784 2.90e-05 a.tt.ATaA..atcgTtCgcGt.a
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7785 3.80e-03 actTtcgcAtGgaAg
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7990 8.50e+02 A.gaTGgta
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7991 2.00e+03 AgAAgGgagGa
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for RSP_3347

RSP_3347 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Methionine synthase I (cobalamin-dependent), methyltransferase domain cog/ cog
methionine synthase activity go/ molecular_function
homocysteine S-methyltransferase activity go/ molecular_function
methionine biosynthetic process go/ biological_process
cobalamin binding go/ molecular_function
cobalt ion binding go/ molecular_function
Cysteine and methionine metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Module neighborhood information for RSP_3347

RSP_3347 has total of 33 gene neighbors in modules 32, 135
Gene neighbors (33)
Gene Common Name Description Module membership
RSP_0992 phaA/B pH adaption potassium efflux system, PhaA/B subunit (NCBI) 32, 361
RSP_0993 phaC pH adaption potassium efflux system, PhaC subunit (NCBI) 32, 361
RSP_0994 phaD pH adaption potassium efflux system, PhaD subunit (NCBI) 32, 361
RSP_0995 phaE pH adaption potassium efflux system, PhaE subunit (NCBI) 32, 361
RSP_0996 phaF pH adaption potassium efflux system, PhaF subunit (NCBI) 32, 361
RSP_0997 phaG pH adaption potassium efflux system, PhaG subunit (NCBI) 32, 361
RSP_1602 RSP_1602 TRAP-T family transporter, DctM (12TMs) subunit (NCBI) 32, 77
RSP_1604 RSP_1604 TRAP-T family transporter, DctQ (4TMs) subunit (NCBI) 32, 77
RSP_1605 RSP_1605 TRAP-T family transporter, periplasmic binding protein, DctP (NCBI) 32, 77
RSP_1606 RSP_1606 Putative regulatory protein, GntR family (NCBI) 32, 214
RSP_1608 RSP_1608 Putative Zn-dependent dehydrogenase (NCBI) 32, 214
RSP_1609 RSP_1609 Putative altronate dehydrogenase (NCBI) 32, 214
RSP_1610 RSP_1610 altronate hydrolase (NCBI) 32, 214
RSP_2273 RSP_2273 putative anaerobic phenylacetate CoA ligase (NCBI) 135, 186
RSP_2274 RSP_2274 ABC branched amino acid transporter family, ATPase subunit (NCBI) 135, 186
RSP_2275 RSP_2275 ABC branched amino acid transporter family, periplasmic substrate-binding subunit (NCBI) 135, 186
RSP_2276 RSP_2276 ABC branched amino acid transporter family, inner membrane subunit (NCBI) 135, 186
RSP_2277 RSP_2277 ABC branched amino acid transporter family, inner membrane subunit (NCBI) 135, 186
RSP_2278 RSP_2278 ABC branched amino acid transporter family, ATPase subunit (NCBI) 135, 186
RSP_2365 RSP_2365 ABC sugar (ribose) transporter, periplasmic substrate-binding subunit (NCBI) 135, 255
RSP_2366 RSP_2366 ABC sugar (ribose) transporter, fused ATPase subunits (NCBI) 135, 255
RSP_2367 RSP_2367 ABC sugar (ribose) transporter, inner membrane subunit (NCBI) 135, 255
RSP_2368 RSP_2368 ABC sugar (ribose) transporter, inner membrane subunit (NCBI) 135, 255
RSP_2370 RSP_2370 putative sugar kinase (NCBI) 135, 255
RSP_2371 RSP_2371 3-oxoacyl-(acyl-carrier protein) reductase / Short-chain dehydrogenase/reductase SDR (NCBI) 135, 325
RSP_2372 RSP_2372 aldehyde dehydrogenase (NAD-dependent) (NCBI) 135, 380
RSP_2373 RSP_2373 Putative Transporter, Major facilitator superfamily (MFS) (NCBI) 135, 265
RSP_3346 RSP_3346 5-methyltetrahydrofolate--homocysteine methyltransferase (NCBI) 32, 135
RSP_3347 RSP_3347 methionine synthase, 5-methyltetrahydrofolate--homocysteine methyltransferase (NCBI) 32, 135
RSP_3696 cysA ABC sulfate/thiosulfate transporter, ATPase subunit CysA (NCBI) 32, 86
RSP_3697 cysP ABC sulfate/thiosulfate transporter, periplasmic binding protein CysP (NCBI) 32, 86
RSP_3698 cysT ABC sulfate/thiosulfate transporter, inner membrane subunit CysT (NCBI) 32, 86
RSP_3699 cysW ABC sulfate/thiosulfate transporter, inner membrane subunit CysW (NCBI) 32, 86
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.

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.

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
  • 6. Visualisation legend
Comments for RSP_3347
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

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
  • 6. Visualisation legend