Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1785

Putative transcriptional regulatory protein (NCBI)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1785
(Mouseover regulator name to see its description)

RSP_1785 is regulated by 20 influences and regulates 9 modules.
Regulators for RSP_1785 (20)
Regulator Module Operator
RSP_0032 308 tf
RSP_0327 308 tf
RSP_1034 308 tf
RSP_1055 308 tf
RSP_1272 308 tf
RSP_1550 308 tf
RSP_1741 308 tf
RSP_1890 308 tf
RSP_1915 308 tf
RSP_2606 308 tf
RSP_3029 308 tf
RSP_1032 76 tf
RSP_1139 76 tf
RSP_1243 76 tf
RSP_1272 76 tf
RSP_1785 76 tf
RSP_2591 76 tf
RSP_3029 76 tf
RSP_3341 76 tf
RSP_3731 76 tf

Warning: RSP_1785 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
7872 1.20e-08 aa.aTtgttggAAACGTTtct
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7873 8.70e-06 aTCcaccGCaaAGaCACcAaAGAC
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8330 8.50e-05 aaAcgttTcctcCaaGaaTtTtC
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8331 6.40e+00 TATGGatTcatCAtAGCGGAA
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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_1785

RSP_1785 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for RSP_1785

RSP_1785 has total of 48 gene neighbors in modules 76, 308
Gene neighbors (48)
Gene Common Name Description Module membership
RSP_0025 RSP_0025 probable NAD(P)-dependent oxidoreductase (NCBI) 227, 308
RSP_0026 RSP_0026 Probable epimerase/dehydratase (NCBI) 227, 308
RSP_0177 RSP_0177 FAD/FMN-containing dehydrogenases (NCBI) 242, 308
RSP_0412 RSP_0412 putative phosphatase (NCBI) 207, 308
RSP_0415 RSP_0415 sigma-24 (NCBI) 308, 381
RSP_0419 RSP_0419 hypothetical protein (NCBI) 10, 308
RSP_0469 RSP_0469 hypothetical protein (NCBI) 227, 308
RSP_0491 hupT Hydrogen uptake histidine-kinase (NCBI) 308, 329
RSP_1032 RSP_1032 possible O6-methylguanine-DNA methyltransferase (NCBI) 76, 107
RSP_1097 RSP_1097 putative zinc protease (NCBI) 262, 308
RSP_1198 RSP_1198 hypothetical protein (NCBI) 196, 308
RSP_1211 RSP_1211 None 99, 308
RSP_1234 aroE putative shikimate 5-dehydrogenase (NCBI) 107, 308
RSP_1242 RSP_1242 hypothetical protein (NCBI) 76, 278
RSP_1243 RSP_1243 transcriptional regulator, LacI family (NCBI) 76, 278
RSP_1244 RSP_1244 putative IolE, Sugar phosphate isomerases/epimerases (NCBI) 76, 278
RSP_1245 RSP_1245 predicted oxidoreductase, Gfo/Idh/MocA family (NCBI) 76, 278
RSP_1247 RSP_1247 ABC sugar transporter, ATPase subunit (NCBI) 76, 278
RSP_1249 RSP_1249 ABC ribose transporter, periplasmic solute-binding protein (NCBI) 76, 278
RSP_1353 RSP_1353 hypothetical protein (NCBI) 197, 308
RSP_1374 lpsB putative lipopolysaccharide core biosynthesis mannosyltransferase protein (NCBI) 278, 308
RSP_1387 RSP_1387 AMP nucleosidase (NCBI) 7, 308
RSP_1538 RSP_1538 probable glucose-1-phosphate cytidylyltransferase (NCBI) 114, 308
RSP_1539 RSP_1539 Glycosyl transferase, family 2 (NCBI) 114, 308
RSP_1646 RSP_1646 possible transmembrane protein (NCBI) 233, 308
RSP_1785 RSP_1785 Putative transcriptional regulatory protein (NCBI) 76, 308
RSP_1786 fruB Multi-component fructose specific PTS system protein, (PtsI, Hpr, and IIA domains) (NCBI) 76, 308
RSP_1787 fruK Probable 1-phosphofructokinase (NCBI) 76, 308
RSP_1788 fruA PTS system, fructose-specificIIBC component (NCBI) 76, 308
RSP_1862 RSP_1862 Dihydropteroate synthase, DHPS (NCBI) 184, 308
RSP_1863 RSP_1863 Phosphoglucomutase/phosphomannomutase (NCBI) 280, 308
RSP_1928 dnaB Replicative DNA helicase, DnaB (NCBI) 76, 234
RSP_2014 RSP_2014 hypothetical protein (NCBI) 287, 308
RSP_2018 RSP_2018 hypothetical protein (NCBI) 308, 323
RSP_2112 ftsQ cell division septal protein FtsQ (NCBI) 308, 349
RSP_2692 RSP_2692 acyltransferase domain (LPS) (NCBI) 76, 96
RSP_2771 RSP_2771 putative Exopolyphosphatase (NCBI) 262, 308
RSP_2772 ftsJ 23S rRNA methylase (NCBI) 127, 308
RSP_2892 RSP_2892 hypothetical protein (NCBI) 185, 308
RSP_2958 RSP_2958 hypothetical protein (NCBI) 288, 308
RSP_3046 dorC DMSO/TMAO pentaheme cytochrome c subunit (NCBI) 155, 308
RSP_3047 dorB DMSO-membrane protein (NCBI) 155, 308
RSP_3048 dorA DMSO/TMAO-reductase (NCBI) 155, 308
RSP_3049 moeA Molybdenum cofactor biosynthesis protein (NCBI) 155, 308
RSP_3050 moaA Molybdenum cofactor biosynthesis protein A (NCBI) 168, 308
RSP_3340 rarD possible transporter, RarD, DMT superfamily (NCBI) 133, 308
RSP_3363 RSP_3363 hypothetical protein (NCBI) 145, 308
RSP_3679 RSP_3679 hypothetical protein (NCBI) 308, 329
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_1785
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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