Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2689 soxA

putative sarcosine oxidase, alpha subunit (NCBI)

CircVis
Functional Annotations (10)
Function System
Uncharacterized NAD(FAD)-dependent dehydrogenases cog/ cog
aminomethyltransferase activity go/ molecular_function
cytoplasm go/ cellular_component
electron transport go/ biological_process
glycine catabolic process go/ biological_process
sarcosine oxidase activity go/ molecular_function
tetrahydrofolate metabolic process go/ biological_process
Glycine serine and threonine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
soxA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2689
(Mouseover regulator name to see its description)

RSP_2689 is regulated by 13 influences and regulates 0 modules.
Regulators for RSP_2689 soxA (13)
Regulator Module Operator
RSP_0415 172 tf
RSP_2346 172 tf
RSP_2888 172 tf
RSP_3238 172 tf
RSP_3341 172 tf
RSP_1297 171 tf
RSP_1518 171 tf
RSP_1550 171 tf
RSP_1890 171 tf
RSP_3202 171 tf
RSP_3238 171 tf
RSP_3684 171 tf
RSP_3686 171 tf

Warning: RSP_2689 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
8062 2.00e-01 aa.tcaggggAaaa.agCGttaTC
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8063 1.70e+01 aTATcTccgGaGgAC
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8064 8.40e+01 CAatCC.t.ttgtaA
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8065 3.10e+02 Tg.gcagAgGatgtatcGcaTgt
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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_2689

RSP_2689 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Uncharacterized NAD(FAD)-dependent dehydrogenases cog/ cog
aminomethyltransferase activity go/ molecular_function
cytoplasm go/ cellular_component
electron transport go/ biological_process
glycine catabolic process go/ biological_process
sarcosine oxidase activity go/ molecular_function
tetrahydrofolate metabolic process go/ biological_process
Glycine serine and threonine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
soxA tigr/ tigrfam
Module neighborhood information for RSP_2689

RSP_2689 has total of 37 gene neighbors in modules 171, 172
Gene neighbors (37)
Gene Common Name Description Module membership
RSP_0217 int possible phage-related integrase (NCBI) 171, 309
RSP_0258 pufA LHI alpha, Light-harvesting B875 protein (NCBI) 172, 377
RSP_0314 pucB LHII beta, light-harvesting B800/850 protein (NCBI) 172, 377
RSP_0430 cobD cobalamin biosynthesis protein CobD (NCBI) 97, 171
RSP_0476 RSP_0476 L-fuculose-phosphate aldolase (NCBI) 27, 172
RSP_0549 RSP_0549 hypothetical protein (NCBI) 71, 171
RSP_0612 RSP_0612 RhtB family transporter (NCBI) 35, 171
RSP_0885 SseA Thiosulfate sulfurtransferase, Rhodanese-like (NCBI) 71, 171
RSP_1024 RSP_1024 Putative MoxR family protein (NCBI) 171, 200
RSP_1277 RSP_1277 hypothetical protein (NCBI) 172, 248
RSP_1295 RSP_1295 putative acyl-CoA dehydrogenase (NCBI) 82, 171
RSP_1297 RSP_1297 transcriptional regulator, LysR family (NCBI) 171, 285
RSP_1412 RSP_1412 TRAP-T family transporter with fused DctQ/DctM subunits (NCBI) 171, 195
RSP_1601 RSP_1601 hypothetical protein (NCBI) 27, 172
RSP_1768 RSP_1768 Aminotransferase class IV , putative D-alanine aminotransferase (NCBI) 112, 171
RSP_1769 RSP_1769 Mandelate racemase / muconate lactonizing enzyme (NCBI) 112, 171
RSP_1770 RSP_1770 hypothetical protein (NCBI) 112, 171
RSP_1817 RSP_1817 hypothetical protein (NCBI) 172, 377
RSP_1818 feoB Fe2+ transport system protein B (NCBI) 172, 377
RSP_1819 feoA1 ferrous iron transport protein A (NCBI) 172, 377
RSP_1984 RSP_1984 histidinol-phosphate-aminotransferase (NCBI) 107, 171
RSP_2222 RSP_2222 hypothetical protein (NCBI) 158, 171
RSP_2223 RSP_2223 AcrB/AcrD/AcrF multidrug efflux pump (NCBI) 171, 340
RSP_2224 RSP_2224 multidrug efflux pump, membrane fusion protein (MFP) family (NCBI) 117, 171
RSP_2688 soxD putative sarcosine oxidase delta subunit protein (NCBI) 21, 172
RSP_2689 soxA putative sarcosine oxidase, alpha subunit (NCBI) 171, 172
RSP_2690 RSP_2690 putative sarcosine oxidase gamma subunit (NCBI) 171, 172
RSP_2749 RSP_2749 putative P4-family integrase (NCBI) 27, 172
RSP_3210 qxtB Quinol oxidase subunit II QxtB (NCBI) 172, 237
RSP_3212 qxtA Quinol oxidase subunit I QxtA (NCBI) 172, 237
RSP_3341 RSP_3341 Protein of unknown function UPF0074 (NCBI) 85, 172
RSP_3364 proC Pyrroline-5-carboxylate reductase (NCBI) 102, 171
RSP_3365 csaA Protein secretion chaperonine (NCBI) 102, 171
RSP_3366 RSP_3366 D-isomer specific 2-hydroxyacid dehydrogenase (NCBI) 102, 171
RSP_3686 RSP_3686 transcriptional regulator, LacI family (NCBI) 171, 216
RSP_3687 RSP_3687 ABC sugar transporter, periplasmic binding protein (NCBI) 57, 171
RSP_3688 RSP_3688 ABC sugar transporter, ATPase subunit (NCBI) 57, 171
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_2689
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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