Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0413

two component diguanylate cyclase (NCBI)

CircVis
Functional Annotations (9)
Function System
Response regulator containing a CheY-like receiver domain and a GGDEF domain cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
cyclic nucleotide biosynthetic process go/ biological_process
phosphorus-oxygen lyase activity go/ molecular_function
intracellular signal transduction go/ biological_process
Two-component system kegg/ kegg pathway
GGDEF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0413
(Mouseover regulator name to see its description)

RSP_0413 is regulated by 27 influences and regulates 0 modules.
Regulators for RSP_0413 (27)
Regulator Module Operator
RSP_0607 137 tf
RSP_0641 137 tf
RSP_1014 137 tf
RSP_1286 137 tf
RSP_1607 137 tf
RSP_1776 137 tf
RSP_1790 137 tf
RSP_1871 137 tf
RSP_2867 137 tf
RSP_2889 137 tf
RSP_3024 137 tf
RSP_3064 137 tf
RSP_3124 137 tf
RSP_3322 137 tf
RSP_3385 137 tf
RSP_3464 137 tf
RSP_3684 137 tf
RSP_0641 236 tf
RSP_1014 236 tf
RSP_1055 236 tf
RSP_1231 236 tf
RSP_1776 236 tf
RSP_1871 236 tf
RSP_2867 236 tf
RSP_3322 236 tf
RSP_3464 236 tf
RSP_3684 236 tf

Warning: RSP_0413 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
7994 9.60e+00 GaTcc.TtTC
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7995 2.50e-01 CCGGaatTCcT
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8190 2.50e+01 TgaatttcaGGCCCT
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8191 5.30e+02 CggtgacactGGAttt.acG
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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_0413

RSP_0413 is enriched for 9 functions in 3 categories.
Module neighborhood information for RSP_0413

RSP_0413 has total of 52 gene neighbors in modules 137, 236
Gene neighbors (52)
Gene Common Name Description Module membership
RSP_0413 RSP_0413 two component diguanylate cyclase (NCBI) 137, 236
RSP_0462 RSP_0462 hypothetical protein (NCBI) 111, 236
RSP_0515 RSP_0515 hypothetical protein (NCBI) 137, 217
RSP_0516 RSP_0516 hypothetical protein (NCBI) 137, 217
RSP_0517 RSP_0517 hypothetical protein (NCBI) 137, 217
RSP_0518 RSP_0518 putative glycosyltransferase protein (NCBI) 137, 217
RSP_0523 RSP_0523 hypothetical protein (NCBI) 137, 217
RSP_0919 RSP_0919 Short-chain dehydrogenase/reductase SDR (NCBI) 137, 150
RSP_1010 RSP_1010 possible esterase/lipase/thioesterase (NCBI) 196, 236
RSP_1014 RSP_1014 sigma24 (NCBI) 54, 236
RSP_1114 RSP_1114 Hemolysin-type calcium-binding toxin (NCBI) 28, 236
RSP_1117 RSP_1117 hypothetical protein (NCBI) 137, 246
RSP_1120 RSP_1120 protein secretion protein, HlyD family, membrane fusion protein (NCBI) 137, 246
RSP_1357 RSP_1357 cytoplasmic sensor hybrid histidine kinase (NCBI) 74, 137
RSP_1428 RSP_1428 Possible Pre (Mob) type recombination enzyme (NCBI) 73, 236
RSP_1530 RSP_1530 hypothetical protein (NCBI) 137, 196
RSP_1638 RSP_1638 hypothetical protein (NCBI) 233, 236
RSP_1643 RSP_1643 hypothetical protein (NCBI) 236, 300
RSP_1662 RSP_1662 Integrase/recombinase (NCBI) 236, 380
RSP_1821 RSP_1821 Molybdopterin-containing oxidoreductase, probable formate dehydrogenase (NCBI) 38, 137
RSP_1872 RSP_1872 Glycosyl transferase, family 2 (NCBI) 236, 238
RSP_1955 RSP_1955 hypothetical protein (NCBI) 124, 236
RSP_1968 RSP_1968 Possible integrase/recombinase (NCBI) 236, 238
RSP_2067 RSP_2067 putative prophage LambdaSo, major capsid protein, HK97 family (NCBI) 137, 191
RSP_2069 RSP_2069 putative phage portal protein, HK97 family (NCBI) 137, 191
RSP_2177 RSP_2177 hypothetical protein (NCBI) 137, 191
RSP_2292 RSP_2292 None 74, 137
RSP_2378 cypC putative fatty acid beta hydroxylase (cytochrome P450) (NCBI) 236, 238
RSP_2468 RSP_2468 putative portal protein (NCBI) 193, 236
RSP_2469 RSP_2469 hypothetical protein (NCBI) 193, 236
RSP_2470 RSP_2470 putative prohead protease (NCBI) 193, 236
RSP_2589 RSP_2589 hypothetical protein (NCBI) 236, 338
RSP_2757 RSP_2757 hypothetical protein (NCBI) 236, 246
RSP_2789 RSP_2789 hypothetical protein (NCBI) 236, 282
RSP_2791 RSP_2791 hypothetical protein (NCBI) 168, 236
RSP_3014 RSP_3014 putative aldolase protein (NCBI) 137, 304
RSP_3016 RSP_3016 Possible phenol degradation enzyme (NCBI) 137, 300
RSP_3019 RSP_3019 putative hydrolase (NCBI) 137, 300
RSP_3021 RSP_3021 putative catechol 2,3-dioxygenase (NCBI) 137, 300
RSP_3063 RSP_3063 AMP-dependent synthetase and ligase (NCBI) 74, 137
RSP_3100 RSP_3100 hypothetical protein (NCBI) 137, 236
RSP_3206 RSP_3206 Putative xanthine dehydrogenase (NCBI) 74, 236
RSP_3258 RSP_3258 ABC peptide transporter, inner membrane subunit (NCBI) 236, 282
RSP_3259 RSP_3259 Transcription antitermination protein (NCBI) 77, 236
RSP_3338 RSP_3338 ABC spermidine/putrescine transporter, ATPase subunit (NCBI) 236, 251
RSP_3380 RSP_3380 hypothetical protein (NCBI) 77, 236
RSP_3427 RSP_3427 hypothetical protein (NCBI) 137, 238
RSP_3623 RSP_3623 putative integrase (NCBI) 137, 191
RSP_3763 RSP_3763 hypothetical protein (NCBI) 137, 138
RSP_3786 RSP_3786 hypothetical protein (NCBI) 141, 236
RSP_3787 RSP_3787 hypothetical protein (NCBI) 236, 285
RSP_3791 RSP_3791 hypothetical protein (NCBI) 137, 138
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_0413
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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