Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2780 oxyR

Transcriptional regulator, OxyR, LysR family (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2780
(Mouseover regulator name to see its description)

RSP_2780 is regulated by 24 influences and regulates 12 modules.
Regulators for RSP_2780 oxyR (24)
Regulator Module Operator
RSP_0071 55 tf
RSP_0443 55 tf
RSP_1032 55 tf
RSP_1518 55 tf
RSP_2572 55 tf
RSP_2719 55 tf
RSP_2780 55 tf
RSP_2800 55 tf
RSP_2950 55 tf
RSP_2963 55 tf
RSP_3064 55 tf
RSP_3238 55 tf
RSP_3686 55 tf
RSP_0607 62 tf
RSP_1014 62 tf
RSP_1435 62 tf
RSP_2780 62 tf
RSP_2867 62 tf
RSP_2882 62 tf
RSP_3322 62 tf
RSP_3339 62 tf
RSP_3400 62 tf
RSP_3464 62 tf
RSP_3528 62 tf

Warning: RSP_2780 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
7830 2.10e-04 aTgCcaAaActCagGcatAtttca
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7831 5.40e-02 Ct.ctgTgt..tg.GAtaaggTca
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7844 5.90e-05 tTATaTtgATaccAAaaaa
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7845 1.90e+01 gCagGATGccCCtgcgaAAGGtcG
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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_2780

RSP_2780 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for RSP_2780

RSP_2780 has total of 47 gene neighbors in modules 55, 62
Gene neighbors (47)
Gene Common Name Description Module membership
RSP_0027 RSP_0027 hypothetical protein (NCBI) 62, 251
RSP_0172 RSP_0172 Predicted transcriptional regulators (NCBI) 38, 62
RSP_0226 RSP_0226 Naringenin-chalcone synthase (NCBI) 62, 189
RSP_0456 RSP_0456 hypothetical protein (NCBI) 62, 380
RSP_0751 RSP_0751 hypothetical protein (NCBI) 62, 97
RSP_1435 RSP_1435 regulatory protein TetR family (NCBI) 62, 97
RSP_1437 RSP_1437 ABC Fe+3 hydroxamate (ferrichrome) transporter, ATPase subunit (NCBI) 24, 55
RSP_1438 RSP_1438 ABC Fe+3 hydroxamate (ferrichrome) transporter, fused inner membrane subunits (NCBI) 24, 55
RSP_1439 RSP_1439 ABC Fe+3 hydroxamate (ferrichrome) transporter, periplasmic siderophore binding protein (NCBI) 24, 55
RSP_1440 RSP_1440 TonB dependent, hydroxamate-type ferrisiderophore, outer membrane receptor (NCBI) 24, 55
RSP_1446 RSP_1446 Putative sugar kinase (NCBI) 62, 89
RSP_1618 RSP_1618 hypothetical protein (NCBI) 62, 304
RSP_1888 RSP_1888 possible acetyltransferase (GNAT) family (NCBI) 38, 62
RSP_1923 bioB Biotin synthase (NCBI) 62, 292
RSP_1996 RSP_1996 Putative Competence protein (NCBI) 62, 380
RSP_2032 RSP_2032 putative hypothetical Gifsy-1 prophage protein (NCBI) 62, 105
RSP_2649 RSP_2649 Putative Zn-dependent protease (NCBI) 62, 285
RSP_2779 catA Catalase (NCBI) 55, 301
RSP_2780 oxyR Transcriptional regulator, OxyR, LysR family (NCBI) 55, 62
RSP_2799 RSP_2799 Putative Zinc-containing alcohol dehydrogenase (NCBI) 62, 379
RSP_2882 RSP_2882 two component transcriptional regulator, LuxR family (NCBI) 62, 381
RSP_2913 RSP_2913 ABC Fe+3 siderophore transporter, periplasmic substrate-binding protein (NCBI) 55, 232
RSP_3020 RSP_3020 hypothetical protein (NCBI) 38, 62
RSP_3027 rdxA RdxA, iron-sulfur cluster-binding protein (NCBI) 62, 196
RSP_3056 RSP_3056 TonB dependent-iron siderophore receptor (NCBI) 24, 55
RSP_3079 RSP_3079 ABC Fe+3 siderophore transporter, periplasmic substrate-binding protein (NCBI) 55, 232
RSP_3081 RSP_3081 ABC multidrug efflux transporter, fused ATPase and inner membrane subunits (NCBI) 24, 55
RSP_3109 RSP_3109 transcriptional regulator, MarR family (NCBI) 62, 285
RSP_3110 RSP_3110 Putative Glutathione S-transferase (NCBI) 62, 342
RSP_3111 RSP_3111 Putative Glutathione S-transferase (NCBI) 62, 285
RSP_3112 RSP_3112 hypothetical protein (NCBI) 62, 285
RSP_3220 RSP_3220 ABC ferric siderophore transporter, inner membrane subunit (NCBI) 24, 55
RSP_3221 RSP_3221 ABC ferric siderophore transporter, inner membrane subunit (NCBI) 24, 55
RSP_3222 RSP_3222 ABC ferric siderophore transporter, ATPase subunit (NCBI) 24, 55
RSP_3278 RSP_3278 Von Willebrand domain containing protein (NCBI) 62, 116
RSP_3292 RSP_3292 Glucose-methanol-choline oxidoreductase (NCBI) 17, 55
RSP_3293 RSP_3293 ABC branched-chain amino acid transporter, inner membrane subunit (NCBI) 17, 55
RSP_3294 RSP_3294 ABC branched-chain amino acid transporter, inner membrane subunit (NCBI) 17, 55
RSP_3295 RSP_3295 ABC branched-chain amino acid transporter, ATPase subunit (NCBI) 17, 55
RSP_3296 RSP_3296 ABC branched-chain amino acid transporter, ATPase subunit (NCBI) 17, 55
RSP_3297 RSP_3297 ABC branched-chain amino acid transporter, periplasmic binding protein (NCBI) 17, 55
RSP_3369 RSP_3369 Asp-tRNA Asn/Glu-tRNA Gln amidotransferase subunit A (NCBI) 55, 364
RSP_3370 RSP_3370 TRAP-T family transporter, DctM (12 TMs) subunit (NCBI) 55, 364
RSP_3371 RSP_3371 TRAP-T family transporter, small (4 TMs) inner membrane subunit (NCBI) 55, 364
RSP_3372 RSP_3372 TRAP-T family transporter, periplasmic binding protein (NCBI) 37, 55
RSP_3499 RSP_3499 H+-transporting two-sector ATPase, alpha/beta subunit (NCBI) 38, 62
RSP_3617 RSP_3617 hypothetical protein (NCBI) 38, 62
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_2780
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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