Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3148

putative succinate dehydrogenase cytochrome b-556 subunit (NCBI)

CircVis
Functional Annotations (14)
Function System
succinate dehydrogenase activity go/ molecular_function
tricarboxylic acid cycle go/ biological_process
electron transport go/ biological_process
plasma membrane succinate dehydrogenase complex go/ cellular_component
Citrate cycle (TCA cycle) kegg/ kegg pathway
Oxidative phosphorylation kegg/ kegg pathway
Toluene degradation kegg/ kegg pathway
Butanoate metabolism kegg/ kegg pathway
Carbon fixation pathways in prokaryotes kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Two-component system kegg/ kegg pathway
succ_dehyd_cytB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3148
(Mouseover regulator name to see its description)

RSP_3148 is regulated by 10 influences and regulates 0 modules.
Regulators for RSP_3148 (10)
Regulator Module Operator
RSP_1231 251 tf
RSP_2027 251 tf
RSP_3700 251 tf
RSP_0386 44 tf
RSP_1231 44 tf
RSP_1518 44 tf
RSP_1790 44 tf
RSP_3505 44 tf
RSP_3676 44 tf
RSP_3694 44 tf

Warning: RSP_3148 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
7808 5.10e-12 aagAAactCtggaaaAatgAgaaT
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7809 1.20e-04 aCcCAcATaAaCaataTcaTTGAC
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8220 1.30e-04 TTt.gctcaGtTtacCtTtCgAT
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8221 1.30e-02 ttCtTcCtCcgccagaa.gtctg
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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_3148

RSP_3148 is enriched for 14 functions in 4 categories.
Enrichment Table (14)
Function System
succinate dehydrogenase activity go/ molecular_function
tricarboxylic acid cycle go/ biological_process
electron transport go/ biological_process
plasma membrane succinate dehydrogenase complex go/ cellular_component
Citrate cycle (TCA cycle) kegg/ kegg pathway
Oxidative phosphorylation kegg/ kegg pathway
Toluene degradation kegg/ kegg pathway
Butanoate metabolism kegg/ kegg pathway
Carbon fixation pathways in prokaryotes kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Two-component system kegg/ kegg pathway
succ_dehyd_cytB tigr/ tigrfam
Module neighborhood information for RSP_3148

RSP_3148 has total of 45 gene neighbors in modules 44, 251
Gene neighbors (45)
Gene Common Name Description Module membership
RSP_0027 RSP_0027 hypothetical protein (NCBI) 62, 251
RSP_0028 RSP_0028 Putative short-chain dehydrogenase/reductase (NCBI) 246, 251
RSP_1142 RSP_1142 hypothetical membrane protein (NCBI) 44, 325
RSP_1373 RSP_1373 Major facilitator superfamily (MFS) transporter (NCBI) 28, 44
RSP_1689 RSP_1689 hypothetical protein (NCBI) 28, 44
RSP_2080 RSP_2080 Putative Tyrosine recombinase (NCBI) 251, 340
RSP_2166 putA Bifunctional putA protein; Proline dehydrogenase / Delta-1-pyrroline-5-carboxylate dehydrogenase (NCBI) 38, 251
RSP_2250 RSP_2250 hypothetical protein (NCBI) 44, 340
RSP_2539 RSP_2539 ABC transporter, ATPase subunit (NCBI) 17, 44
RSP_2758 RSP_2758 hypothetical protein (NCBI) 246, 251
RSP_2760 RSP_2760 hypothetical protein (NCBI) 246, 251
RSP_2992 RSP_2992 hypothetical protein (NCBI) 44, 355
RSP_3143 RSP_3143 hypothetical protein (NCBI) 44, 251
RSP_3144 RSP_3144 hypothetical protein (NCBI) 44, 251
RSP_3145 ttdB Putative Tartrate dehydratase beta subunit (NCBI) 44, 251
RSP_3146 ttdA Putative Tartrate dehydratase alpha subunit (NCBI) 44, 251
RSP_3147 sdhA putative succinate dehydrogenase/fumarate reductase, flavoprotein subunit (NCBI) 44, 251
RSP_3148 RSP_3148 putative succinate dehydrogenase cytochrome b-556 subunit (NCBI) 44, 251
RSP_3149 RSP_3149 putative succinate dehydrogenase membrane anchor (NCBI) 44, 251
RSP_3150 frdB Succinate dehydrogenase/fumarate reductase Fe-S protein subunit (NCBI) 44, 251
RSP_3153 RSP_3153 ABC nitrate/sulfonate/bicarbonate transporter family, inner membrane subunit (NCBI) 110, 251
RSP_3154 RSP_3154 ABC nitrate/sulfonate/bicarbonate transporter family, ATPase subunit (NCBI) 105, 251
RSP_3155 RSP_3155 Thiamine pyrophosphate-requiring enzyme (NCBI) 251, 273
RSP_3334 RSP_3334 HyuE hydantoin racemase (NCBI) 44, 103
RSP_3335 RSP_3335 ABC spermidine/putrescine transporter, inner membrane subunit (NCBI) 44, 141
RSP_3336 RSP_3336 ABC spermidine/putrescine transporter, inner membrane subunit (NCBI) 44, 141
RSP_3338 RSP_3338 ABC spermidine/putrescine transporter, ATPase subunit (NCBI) 236, 251
RSP_3420 RSP_3420 Methyl-accepting chemotaxis protein (NCBI) 77, 251
RSP_3422 RSP_3422 hypothetical protein (NCBI) 251, 323
RSP_3500 RSP_3500 ABC sugar transporter, periplasmic binding protein (NCBI) 44, 303
RSP_3501 RSP_3501 ABC sugar transporter, inner membrane subunit (NCBI) 44, 303
RSP_3502 RSP_3502 ABC sugar transporter, inner membrane subunit (NCBI) 44, 303
RSP_3503 RSP_3503 ABC sugar transporter, fused ATPase domains (NCBI) 44, 303
RSP_3505 RSP_3505 transcriptional regulator, DeoR family (NCBI) 44, 303
RSP_3506 RSP_3506 probable sugar kinase, EGGY family protein (NCBI) 44, 303
RSP_3574 hutH putative histidine ammonia-lyase (NCBI) 44, 105
RSP_3675 RSP_3675 Esterase/lipase/thioesterase (NCBI) 44, 323
RSP_3676 RSP_3676 transcriptional regulator, GntR family (NCBI) 44, 105
RSP_3677 RSP_3677 ABC sugar transporter, ATPase subunit (NCBI) 44, 323
RSP_3700 RSP_3700 transcriptional regulator, LacI family (NCBI) 157, 251
RSP_3701 RSP_3701 ABC sugar transporter, periplasmic binding protein (NCBI) 157, 251
RSP_3702 RSP_3702 ABC sugar transporter, ATPase subunit (NCBI) 157, 251
RSP_3703 RSP_3703 ABC sugar transporter, inner membrane subunit (NCBI) 157, 251
RSP_3704 RSP_3704 ribitol 2-dehydrogenase (NCBI) 157, 251
RSP_3705 RSP_3705 D-ribulokinase (NCBI) 157, 251
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_3148
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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