Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2922

Transcriptional regulator, AraC family (NCBI)

CircVis
Functional Annotations (6)
Function System
Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2922
(Mouseover regulator name to see its description)

RSP_2922 is regulated by 24 influences and regulates 47 modules.
Regulators for RSP_2922 (24)
Regulator Module Operator
RSP_0395 309 tf
RSP_0443 309 tf
RSP_0489 309 tf
RSP_1163 309 tf
RSP_1231 309 tf
RSP_1274 309 tf
RSP_1704 309 tf
RSP_1890 309 tf
RSP_2410 309 tf
RSP_3324 309 tf
RSP_0122 182 tf
RSP_0395 182 tf
RSP_0443 182 tf
RSP_0755 182 tf
RSP_1040 182 tf
RSP_1225 182 tf
RSP_1231 182 tf
RSP_1739 182 tf
RSP_1741 182 tf
RSP_2494 182 tf
RSP_2922 182 tf
RSP_3309 182 tf
RSP_3445 182 tf
RSP_3684 182 tf

Warning: RSP_2922 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
8084 1.10e-05 aaa.gCgg.ggCacAggacGg.aA
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8085 9.00e-03 AActtcgcCcAATTC
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8332 2.70e-08 AatggGgCGag.TTcCcCcTT
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8333 7.00e-03 tCCTgtTTcgCaGgA
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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_2922

RSP_2922 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for RSP_2922

RSP_2922 has total of 47 gene neighbors in modules 182, 309
Gene neighbors (47)
Gene Common Name Description Module membership
RSP_0123 cerI Autoinducer synthesis protein (NCBI) 97, 309
RSP_0124 RSP_0124 hypothetical protein (NCBI) 161, 309
RSP_0217 int possible phage-related integrase (NCBI) 171, 309
RSP_0675 RSP_0675 putative TatD-related deoxyribonuclease (NCBI) 182, 203
RSP_0676 RSP_0676 PhnP-like protein (NCBI) 182, 218
RSP_0882 DapA Dihydrodipicolinate synthetase (NCBI) 182, 372
RSP_0890 RSP_0890 possible protein yrbC precursor (NCBI) 182, 309
RSP_0891 vacJ putative lipoprotein (NCBI) 182, 309
RSP_0892 RSP_0892 ABC protein toxin exporter, fused ATPase and inner membrane domain (NCBI) 182, 309
RSP_0893 RSP_0893 RTX secretion protein D, HlyD family (NCBI) 182, 309
RSP_0929 accD Acetyl-CoA carboxylase carboxyl transferase, beta subunit (NCBI) 309, 360
RSP_1060 rnpA Ribonuclease P protein component (NCBI) 182, 208
RSP_1225 spo0J ParB-like partition protein (NCBI) 87, 182
RSP_1227 parA putative chromosome partitioning protein, ParA (NCBI) 178, 182
RSP_1228 gidB putative GidB, Glucose inhibited division protein (NCBI) 87, 182
RSP_1229 gidA Glucose-inhibited division protein, A family (NCBI) 87, 182
RSP_1230 thdF Predicted GTPase (NCBI) 87, 182
RSP_1231 rho Transcription termination factor rho (NCBI) 43, 182
RSP_1365 RSP_1365 hypothetical protein (NCBI) 182, 323
RSP_1772 accA Acetyl-CoA carboxylase, alpha subunit (NCBI) 48, 182
RSP_1773 RSP_1773 Multidrug efflux pump, SMR family, DMT superfamily (NCBI) 98, 182
RSP_1843 ftsY Signal recognition particle-docking protein FtsY (NCBI) 71, 309
RSP_1864 RSP_1864 hypothetical protein (NCBI) 48, 309
RSP_1948 RSP_1948 Protein of unknown function, HesB/YadR/YfhF (NCBI) 161, 309
RSP_1949 RSP_1949 hypothetical protein (NCBI) 161, 309
RSP_1986 gatB Glutamyl-tRNA amidotransferase subunit B (NCBI) 25, 309
RSP_1991 RSP_1991 Putative Ornithine decarboxylase (NCBI) 309, 365
RSP_1994 gltA Citrate synthase (NCBI) 279, 309
RSP_2169 suhB Inositol monophosphatase family protein (NCBI) 182, 224
RSP_2193 gcvT predicted aminomethyltransferase, tetrahydrofolate dependent (NCBI) 71, 309
RSP_2246 hisB Imidazoleglycerol-phosphate dehydratase (NCBI) 93, 182
RSP_2329 mreB Cell shape determining protein MreB/Mrl (NCBI) 93, 309
RSP_2494 fur Ferric-uptake regulator (NCBI) 75, 182
RSP_2630 gyrA DNA gyrase/topoisomerase IV, subunit A (NCBI) 43, 182
RSP_2646 RSP_2646 None 286, 309
RSP_2718 RSP_2718 possible outer membrane protein (NCBI) 3, 309
RSP_2783 lipA lipoic acid synthetase (NCBI) 161, 309
RSP_2914 RSP_2914 Nucleoside hydrolase (NCBI) 126, 309
RSP_2921 RSP_2921 phospho-2-dehydro-3-deoxyheptonate (NCBI) 182, 309
RSP_2922 RSP_2922 Transcriptional regulator, AraC family (NCBI) 182, 309
RSP_2975 RSP_2975 hypothetical protein (NCBI) 71, 309
RSP_3074 ilvD Dihydroxy-acid and 6-phosphogluconate dehydratase (NCBI) 15, 309
RSP_3585 RSP_3585 Tryptophan synthase beta chain (NCBI) 173, 182
RSP_3597 RSP_3597 CorC/Hlyc family protein with CBS domains (NCBI) 182, 200
RSP_3598 RSP_3598 Protein of unknown function UPF0054 (NCBI) 182, 200
RSP_3820 rpmA Ribosomal protein L27 (NCBI) 169, 309
RSP_3821 RSP_3821 Putative acetyltransferase (NCBI) 297, 309
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_2922
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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