Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2335 wrbA

trp repressor binding protein WrbA, putative (NCBI)

CircVis
Functional Annotations (5)
Function System
Multimeric flavodoxin WrbA cog/ cog
NAD(P)H dehydrogenase (quinone) activity go/ molecular_function
FMN binding go/ molecular_function
oxidoreductase activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2335
(Mouseover regulator name to see its description)

RSP_2335 is regulated by 40 influences and regulates 0 modules.
Regulators for RSP_2335 wrbA (40)
Regulator Module Operator
RSP_0616 124 tf
RSP_0927 124 tf
RSP_1014 124 tf
RSP_1032 124 tf
RSP_1191 124 tf
RSP_1225 124 tf
RSP_1518 124 tf
RSP_1606 124 tf
RSP_1660 124 tf
RSP_1776 124 tf
RSP_1892 124 tf
RSP_2130 124 tf
RSP_2171 124 tf
RSP_2610 124 tf
RSP_2681 124 tf
RSP_2853 124 tf
RSP_2950 124 tf
RSP_3022 124 tf
RSP_3095 124 tf
RSP_3339 124 tf
RSP_0087 368 tf
RSP_0394 368 tf
RSP_0794 368 tf
RSP_1191 368 tf
RSP_1231 368 tf
RSP_1272 368 tf
RSP_1274 368 tf
RSP_1741 368 tf
RSP_1892 368 tf
RSP_1922 368 tf
RSP_2027 368 tf
RSP_2130 368 tf
RSP_2681 368 tf
RSP_2853 368 tf
RSP_3094 368 tf
RSP_3095 368 tf
RSP_3179 368 tf
RSP_3385 368 tf
RSP_3418 368 tf
RSP_3700 368 tf

Warning: RSP_2335 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
7968 2.30e+01 tTCCcg.cggagtttccgcC
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7969 1.30e+03 cccGagtTgCtGtttcCgAtGc
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8432 1.90e+00 cT.CAtga.tTCGgC.AttttctG
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8433 3.20e+03 cGaggaTcTCG
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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_2335

RSP_2335 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Multimeric flavodoxin WrbA cog/ cog
NAD(P)H dehydrogenase (quinone) activity go/ molecular_function
FMN binding go/ molecular_function
oxidoreductase activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for RSP_2335

RSP_2335 has total of 48 gene neighbors in modules 124, 368
Gene neighbors (48)
Gene Common Name Description Module membership
RSP_0138 RSP_0138 hypothetical protein (NCBI) 124, 188
RSP_0235 moaA molybdenum cofactor biosynthesis protein A (NCBI) 132, 368
RSP_0414 RSP_0414 hypothetical protein (NCBI) 124, 281
RSP_0455 RSP_0455 possible NOL1/NOP2/sun family protein (NCBI) 39, 124
RSP_0457 glpR probable glycerol-3-phosphate regulon repressor (NCBI) 39, 124
RSP_0585 osmC osmotically inducible protein OsmC (NCBI) 124, 368
RSP_0753 SspA Salt-stress induced outer membrane protein (NCBI) 280, 368
RSP_0828 RSP_0828 Major facilitator superfamily (MFS) transporter (NCBI) 124, 196
RSP_0855 RSP_0855 hypothetical protein (NCBI) 124, 188
RSP_0944 purU PurU, Formyltetrahydrofolate deformylase (NCBI) 124, 268
RSP_0948 otsA probable OtsA trehalose-6-phosphate synthase (NCBI) 27, 368
RSP_0949 ostB putative trehalose-6-phosphate phosphatase (NCBI) 7, 368
RSP_1015 RSP_1015 Putative membrane protein with von Willebrand (VWA) domain (NCBI) 54, 124
RSP_1129 RSP_1129 hypothetical protein (NCBI) 50, 124
RSP_1159 galU UDP-glucose pyrophosphate (NCBI) 132, 368
RSP_1190 RSP_1190 hypothetical protein (NCBI) 215, 368
RSP_1191 RSP_1191 transcriptional regulator, MarR family (NCBI) 215, 368
RSP_1192 RSP_1192 None 215, 368
RSP_1276 RSP_1276 hypothetical protein (NCBI) 215, 368
RSP_1304 RSP_1304 putative flagellar hook protein (NCBI) 124, 246
RSP_1370 RSP_1370 Alpha amylase, catalytic subdomain (NCBI) 124, 229
RSP_1695 RSP_1695 hypothetical protein (NCBI) 38, 124
RSP_1929 pyrE Orotate phosphoribosyltransferase (NCBI) 124, 311
RSP_1955 RSP_1955 hypothetical protein (NCBI) 124, 236
RSP_1985 RSP_1985 hypothetical protein (NCBI) 48, 368
RSP_2135 RSP_2135 hypothetical protein (NCBI) 124, 156
RSP_2231 RSP_2231 hypothetical protein (NCBI) 181, 368
RSP_2335 wrbA trp repressor binding protein WrbA, putative (NCBI) 124, 368
RSP_2379 RSP_2379 hypothetical protein (NCBI) 181, 368
RSP_2380 catC Catalase (NCBI) 124, 313
RSP_2384 RSP_2384 hypothetical protein (NCBI) 19, 368
RSP_2385 RSP_2385 hypothetical protein (NCBI) 103, 124
RSP_2430 RSP_2430 hypothetical protein (NCBI) 36, 368
RSP_2569 sqdB sulfolipid (UDP-sulfoquinovose) biosynthesis protein (NCBI) 339, 368
RSP_2570 pfpI protease I (NCBI) 124, 150
RSP_2575 RSP_2575 hypothetical protein (NCBI) 38, 124
RSP_2634 ccmH Cytochrome c maturation protein, CcmH (NCBI) 215, 368
RSP_2673 RSP_2673 Glucose dehydrogenase (NCBI) 120, 368
RSP_2681 rpoE sigma factor, RpoE (NCBI) 181, 368
RSP_2766 RSP_2766 Uncharacterized metal-binding protein (NCBI) 73, 124
RSP_2916 RSP_2916 hypothetical protein (NCBI) 124, 181
RSP_3092 RSP_3092 hypothetical protein (NCBI) 202, 368
RSP_3093 RSP_3093 Predicted integral membrane protein (NCBI) 202, 368
RSP_3115 RSP_3115 Conserved hypothetical membrane protein (NCBI) 280, 368
RSP_3204 RSP_3204 putative Oxidoreductase (NCBI) 124, 304
RSP_3205 RSP_3205 putative oxidoreductase subunit (NCBI) 120, 124
RSP_3618 RSP_3618 hypothetical protein (NCBI) 124, 313
RSP_3647 RSP_3647 hypothetical protein (NCBI) 124, 273
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_2335
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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