Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3344

PAS sensor diguanylate cyclase (NCBI)

CircVis
Functional Annotations (5)
Function System
FOG: GGDEF domain cog/ cog
cyclic nucleotide biosynthetic process go/ biological_process
phosphorus-oxygen lyase activity go/ molecular_function
intracellular signal transduction go/ biological_process
GGDEF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3344
(Mouseover regulator name to see its description)

RSP_3344 is regulated by 29 influences and regulates 0 modules.
Regulators for RSP_3344 (29)
Regulator Module Operator
RSP_0755 356 tf
RSP_0794 356 tf
RSP_0999 356 tf
RSP_1055 356 tf
RSP_1660 356 tf
RSP_1866 356 tf
RSP_2351 356 tf
RSP_2533 356 tf
RSP_2950 356 tf
RSP_3165 356 tf
RSP_3238 356 tf
RSP_3341 356 tf
RSP_3621 356 tf
RSP_3748 356 tf
RSP_0316 174 tf
RSP_0402 174 tf
RSP_0623 174 tf
RSP_1243 174 tf
RSP_1550 174 tf
RSP_1669 174 tf
RSP_1892 174 tf
RSP_1922 174 tf
RSP_2171 174 tf
RSP_2591 174 tf
RSP_2610 174 tf
RSP_2681 174 tf
RSP_2867 174 tf
RSP_2939 174 tf
RSP_3464 174 tf

Warning: RSP_3344 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
8068 7.00e+01 aAaGaAa.gccTGctac.aCATct
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8069 2.90e+03 TTGACa
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8410 1.70e-02 atgacacttCaGtGAaaaGA
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8411 3.80e+01 ATATCtggcAAAGGtCAT
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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_3344

RSP_3344 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
FOG: GGDEF domain cog/ cog
cyclic nucleotide biosynthetic process go/ biological_process
phosphorus-oxygen lyase activity go/ molecular_function
intracellular signal transduction go/ biological_process
GGDEF tigr/ tigrfam
Module neighborhood information for RSP_3344

RSP_3344 has total of 61 gene neighbors in modules 174, 356
Gene neighbors (61)
Gene Common Name Description Module membership
RSP_0170 RSP_0170 hypothetical protein (NCBI) 174, 291
RSP_0329 RSP_0329 GAF sensor diguanylate cyclase (GGDEF) (NCBI) 174, 175
RSP_0803 DppF ABC dipeptide transporter, ATPase subunit DppF (NCBI) 174, 175
RSP_0821 RSP_0821 Esterase/lipase/thioesterase (NCBI) 72, 356
RSP_0939 RSP_0939 hypothetical protein (NCBI) 140, 356
RSP_0959 RSP_0959 ATPase (NCBI) 174, 200
RSP_1045 trmD tRNA (guanine-N1-)-methyltransferase (NCBI) 279, 356
RSP_1101 RSP_1101 hypothetical protein (NCBI) 129, 356
RSP_1149 gltD Glutamate synthase (beta subunit) (NCBI) 98, 356
RSP_1152 rnd Ribonuclease D (NCBI) 192, 356
RSP_1154 RSP_1154 hypothetical protein (NCBI) 129, 356
RSP_1155 RSP_1155 OstA-like protein (NCBI) 129, 356
RSP_1361 RSP_1361 hypothetical protein (NCBI) 126, 174
RSP_1499 RSP_1499 Probable gamma-glutamyltranspeptidase (NCBI) 174, 278
RSP_1502 RSP_1502 GAF domain protein (NCBI) 29, 174
RSP_1523 RSP_1523 hypothetical protein (NCBI) 23, 174
RSP_1596 deoB probable phosphopentomutase protein (NCBI) 15, 174
RSP_1597 add adenosine deaminase (NCBI) 15, 174
RSP_1687 hbdA S(+)-beta-hydroxybutyryl CoA dehydrogenase (NCBI) 174, 178
RSP_1690 etfA Electron transfer flavoprotein, alpha subunit (NCBI) 174, 266
RSP_1691 etfB Electron transfer flavoprotein beta-subunit (NCBI) 174, 266
RSP_1777 RSP_1777 Putative electron transfer flavoprotein-ubiquinone oxidoreductase precursor (NCBI) 174, 266
RSP_1830 surf-1 Surf1 protein (NCBI) 126, 356
RSP_1847 PurD Phosphoribosylamine--glycine ligase (NCBI) 160, 356
RSP_1865 RSP_1865 ketol-acid reductoisomerase (NCBI) 261, 356
RSP_1866 RSP_1866 Transcriptional regulator, AsnC family (NCBI) 187, 356
RSP_1867 RSP_1867 transcriptional regulator, AsnC family (NCBI) 189, 356
RSP_2191 pccA Propionyl-CoA carboxylase alpha subunit (NCBI) 121, 356
RSP_2196 RSP_2196 enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxybutyryl-CoA epimerase (NCBI) 174, 216
RSP_2197 RSP_2197 Acetoacetyl-CoA thiolase (NCBI) 174, 216
RSP_2198 RSP_2198 hypothetical protein (NCBI) 66, 174
RSP_2208 RSP_2208 ABC sugar transporter, inner membrane subunit (NCBI) 67, 174
RSP_2209 RSP_2209 ABC sugar transporter, inner membrane subunit (NCBI) 67, 174
RSP_2210 RSP_2210 ABC sugar transporter, fused ATPase subunits (NCBI) 174, 358
RSP_2284 RSP_2284 Histidinol-phosphate aminotransferase (NCBI) 311, 356
RSP_2327 RSP_2327 hypothetical protein (NCBI) 356, 383
RSP_2328 mreC Rod shape-determining protein, MreC (NCBI) 87, 356
RSP_2362 RSP_2362 transcriptional regulator, GntR family (NCBI) 174, 265
RSP_2398 RSP_2398 ABC putrescine transporter, inner membrane subunit (NCBI) 174, 291
RSP_2619 trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (NCBI) 187, 356
RSP_2748 RSP_2748 possible transcriptional regulator, CopG family (NCBI) 152, 356
RSP_2790 RSP_2790 hypothetical protein (NCBI) 84, 356
RSP_2842 trkH1 potassium uptake transporter, transmembrane subunit, TrkH (NCBI) 174, 293
RSP_2912 RSP_2912 Predicted pyrophosphatase (NCBI) 279, 356
RSP_2939 RSP_2939 Predicted transcriptional regulator containing the HTH domain (NCBI) 67, 174
RSP_2940 RSP_2940 hypothetical protein (NCBI) 174, 341
RSP_2970 RSP_2970 Transporter, Major facilitator superfamily (MFS) (NCBI) 231, 356
RSP_3101 RSP_3101 periplasmic sensor diguanylate cyclase/phosphodiesterase (NCBI) 23, 174
RSP_3161 RSP_3161 hypothetical protein (NCBI) 63, 174
RSP_3170 RSP_3170 Demethylmenaquinone methyltransferase (NCBI) 337, 356
RSP_3171 RSP_3171 3-hydroxyisobutyrate dehydrogenase (NCBI) 337, 356
RSP_3172 RSP_3172 hypothetical protein (NCBI) 337, 356
RSP_3200 RSP_3200 Molecular chaperone, DnaK (NCBI) 146, 356
RSP_3227 RSP_3227 Lysine 2,3-aminomutase (NCBI) 289, 356
RSP_3344 RSP_3344 PAS sensor diguanylate cyclase (NCBI) 174, 356
RSP_3345 RSP_3345 hypothetical protein (NCBI) 174, 195
RSP_3593 RSP_3593 hypothetical protein (NCBI) 214, 356
RSP_3607 RSP_3607 hypothetical protein (NCBI) 129, 356
RSP_3777 RSP_3777 hypothetical protein (NCBI) 29, 356
RSP_3826 RSP_3826 hypothetical protein (NCBI) 174, 242
RSP_3827 RSP_3827 Phospholipid/glycerol acyltransferase (NCBI) 174, 293
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_3344
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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