Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2200

transcriptional regulator, MerR family (NCBI)

CircVis
Functional Annotations (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2200
(Mouseover regulator name to see its description)

RSP_2200 is regulated by 12 influences and regulates 21 modules.
Regulators for RSP_2200 (12)
Regulator Module Operator
RSP_0443 266 tf
RSP_0489 266 tf
RSP_1092 266 tf
RSP_2130 266 tf
RSP_2200 266 tf
RSP_0402 66 tf
RSP_0755 66 tf
RSP_1518 66 tf
RSP_2200 66 tf
RSP_2591 66 tf
RSP_2950 66 tf
RSP_2963 66 tf

Warning: RSP_2200 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
7852 1.00e+00 Ttacg.agCGT
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7853 1.60e+03 CctCgtcactGgcCGGcacGAt
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8250 4.90e+01 CtTGtcgtTtt
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8251 1.30e+04 AAGTAAGT
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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_2200

RSP_2200 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for RSP_2200

RSP_2200 has total of 41 gene neighbors in modules 66, 266
Gene neighbors (41)
Gene Common Name Description Module membership
RSP_0154 RSP_0154 3-hydroxyisobutyrate dehydrogenase (NCBI) 37, 66
RSP_0155 RSP_0155 enoyl-CoA hydratase (NCBI) 37, 66
RSP_0156 RSP_0156 Acyl-CoA dehydrogenase (NCBI) 37, 66
RSP_0741 RSP_0741 putative metallo-beta-lactamase family protein (NCBI) 37, 66
RSP_0742 RSP_0742 probable acyl-CoA dehydrogenase (NCBI) 37, 66
RSP_0904 sitA ABC Mn+2/Fe+2 transporter, periplasmic substrate-binding protein SitA (NCBI) 266, 301
RSP_0905 sitB ABC Mn+2/Fe+2 transporter, ATPase subunit SitB (NCBI) 266, 301
RSP_0906 sitC ABC Mn+2/Fe+2 transporter, inner membrane subunit SitC (NCBI) 266, 301
RSP_0908 sitD ABC Mn+2/Fe+2 transporter, inner membrane subunit SitD (NCBI) 266, 301
RSP_1252 RSP_1252 2-nitropropane dioxygenase-like protein (NCBI) 37, 66
RSP_1354 RSP_1354 Thiolase (NCBI) 37, 66
RSP_1382 RSP_1382 radical SAM superfamily protein (NCBI) 266, 268
RSP_1690 etfA Electron transfer flavoprotein, alpha subunit (NCBI) 174, 266
RSP_1691 etfB Electron transfer flavoprotein beta-subunit (NCBI) 174, 266
RSP_1777 RSP_1777 Putative electron transfer flavoprotein-ubiquinone oxidoreductase precursor (NCBI) 174, 266
RSP_2198 RSP_2198 hypothetical protein (NCBI) 66, 174
RSP_2199 RSP_2199 putative acyl-CoA dehydrogenase (NCBI) 66, 266
RSP_2200 RSP_2200 transcriptional regulator, MerR family (NCBI) 66, 266
RSP_2255 RSP_2255 Long-chain-fatty-acid--CoA ligase (NCBI) 37, 66
RSP_2506 ivdH Isovaleryl-CoA dehydrogenase (NCBI) 37, 66
RSP_2508 mccB Methylcrotonyl-CoA carboxylase beta chain (NCBI) 37, 66
RSP_2509 mccA Methylcrotonyl-CoA carboxylase alpha chain (NCBI) 37, 66
RSP_2510 hmgL Hydroxymethylglutaryl-CoA lyase (NCBI) 37, 66
RSP_2511 RSP_2511 enoyl-CoA hydratase/isomerase family protein (NCBI) 37, 66
RSP_2635 RSP_2635 None 37, 66
RSP_2655 RSP_2655 hypothetical protein (NCBI) 37, 66
RSP_3181 RSP_3181 putative fatty-acyl-CoA racemase; CoA-transferase family III (NCBI) 37, 66
RSP_3182 RSP_3182 Acyl-CoA dehydrogenase (NCBI) 37, 66
RSP_3183 RSP_3183 3-hydroxyacyl-CoA dehydrogenase type II (NCBI) 37, 66
RSP_3184 RSP_3184 putative Thiolase (NCBI) 37, 66
RSP_3784 RSP_3784 Peptidase U7 (NCBI) 194, 266
RSP_6047 RSP_6047 hypothetical protein (NCBI) 194, 266
RSP_6053 RSP_6053 putative phage tail-head adaptor (NCBI) 142, 266
RSP_6078 RSP_6078 hypothetical protein (NCBI) 266, 352
RSP_6160 dorY DMSO reductase regulatory protein DorY (NCBI) 266, 364
RSP_6179 RSP_6179 hypothetical protein (NCBI) 266, 364
RSP_6194 RSP_6194 hypothetical protein (NCBI) 194, 266
RSP_6197 RSP_6197 hypothetical protein (NCBI) 266, 364
RSP_6217 cobH precorrin isomerase (NCBI) 266, 364
RSP_6229 RSP_6229 hypothetical protein (NCBI) 33, 266
RSP_6240 RSP_6240 None 194, 266
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_2200
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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