Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2898

putative DNA polymerase III chi subunit (NCBI)

CircVis
Functional Annotations (10)
Function System
DNA polymerase III, chi subunit cog/ cog
DNA binding go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA replication go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
DNA replication kegg/ kegg pathway
Mismatch repair kegg/ kegg pathway
Homologous recombination kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2898
(Mouseover regulator name to see its description)

RSP_2898 is regulated by 28 influences and regulates 0 modules.
Regulators for RSP_2898 (28)
Regulator Module Operator
RSP_0327 4 tf
RSP_0611 4 tf
RSP_0755 4 tf
RSP_0927 4 tf
RSP_1032 4 tf
RSP_1243 4 tf
RSP_1790 4 tf
RSP_2888 4 tf
RSP_3341 4 tf
RSP_3731 4 tf
RSP_0722 175 tf
RSP_1032 175 tf
RSP_1092 175 tf
RSP_1577 175 tf
RSP_1590 175 tf
RSP_1866 175 tf
RSP_1952 175 tf
RSP_2171 175 tf
RSP_2533 175 tf
RSP_2610 175 tf
RSP_2730 175 tf
RSP_2838 175 tf
RSP_2867 175 tf
RSP_2889 175 tf
RSP_2939 175 tf
RSP_3324 175 tf
RSP_3606 175 tf
RSP_3665 175 tf

Warning: RSP_2898 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
7730 1.60e+03 GccctCcCtTGCCgC
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7731 2.20e+03 ccATCCggCC
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8070 4.90e-06 AAAAaATccCccGaaTTcTCCCCG
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8071 3.10e-01 at.cAgcC.CGtCcCgGGTGcGta
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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_2898

RSP_2898 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
DNA polymerase III, chi subunit cog/ cog
DNA binding go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA replication go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
DNA replication kegg/ kegg pathway
Mismatch repair kegg/ kegg pathway
Homologous recombination kegg/ kegg pathway
Module neighborhood information for RSP_2898

RSP_2898 has total of 51 gene neighbors in modules 4, 175
Gene neighbors (51)
Gene Common Name Description Module membership
RSP_0119 RSP_0119 PA-phosphatase related phosphoesterase (NCBI) 2, 4
RSP_0182 RSP_0182 None 95, 175
RSP_0302 ureG Urease accessory protein G (NCBI) 175, 307
RSP_0303 ureF Urease accessory protein UreF (NCBI) 175, 307
RSP_0304 ureE urease accessory protein UreE (NCBI) 175, 307
RSP_0305 RSP_0305 hypothetical protein (NCBI) 175, 307
RSP_0306 RSP_0306 Class I diheme cytochrome c (NCBI) 175, 307
RSP_0327 nnrR Crp-Fnr regulatory protein (NnrR) (NCBI) 4, 126
RSP_0329 RSP_0329 GAF sensor diguanylate cyclase (GGDEF) (NCBI) 174, 175
RSP_0406 RSP_0406 periplasmic sensor diguanylate cyclase (GGDEF) (NCBI) 126, 175
RSP_0407 RSP_0407 putative lactate dehydrogenase (NCBI) 175, 384
RSP_0555 ruvA Holliday junction DNA helicase ruvA (NCBI) 4, 48
RSP_0556 ruvC Holliday junction nuclease RuvC (NCBI) 4, 48
RSP_0803 DppF ABC dipeptide transporter, ATPase subunit DppF (NCBI) 174, 175
RSP_0826 RSP_0826 hypothetical protein (NCBI) 4, 142
RSP_0845 RSP_0845 hypothetical protein (NCBI) 4, 10
RSP_0846 ribA GTP cyclohydrolase II (NCBI) 4, 10
RSP_0894 RSP_0894 hypothetical protein (NCBI) 175, 384
RSP_0895 RSP_0895 phosphodiesterase-like (NCBI) 7, 175
RSP_0943 yhxA probable adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI) 25, 175
RSP_1086 sdh saccharopine dehydrogenase (NAD+, L-lysine forming) (NCBI) 72, 175
RSP_1306 RSP_1306 PAS sensor Signal Tranduction Histidine Kinase (NCBI) 4, 234
RSP_1377 RSP_1377 Carbonic anhydrase (NCBI) 112, 175
RSP_1378 RSP_1378 hypothetical protein (NCBI) 175, 189
RSP_1379 RSP_1379 Cytosol aminopeptidase (NCBI) 175, 384
RSP_1380 RSP_1380 hypothetical protein (NCBI) 7, 175
RSP_1411 RSP_1411 putative membrane protein (NCBI) 2, 4
RSP_1590 RSP_1590 two component, sigma54 specific, transcriptional regulator, fis family (NCBI) 175, 358
RSP_1809 RSP_1809 None 4, 113
RSP_1911 RSP_1911 possible soluble lytic murein transglycosylase (NCBI) 4, 122
RSP_1946 RSP_1946 Cytochrome P450 hydroxylase (NCBI) 175, 381
RSP_1982 RSP_1982 Aminopeptidase N (NCBI) 4, 256
RSP_2012 RSP_2012 NUDIX hydrolase, MutT (NCBI) 175, 242
RSP_2035 RSP_2035 hypothetical protein (NCBI) 4, 82
RSP_2142 RSP_2142 NifS-related protein (NCBI) 4, 10
RSP_2168 RSP_2168 hypothetical protein (NCBI) 126, 175
RSP_2188 RSP_2188 hypothetical protein (NCBI) 175, 214
RSP_2252 RSP_2252 Threonine dehydratase (NCBI) 145, 175
RSP_2253 RSP_2253 predicted hydrolases or acyltransferases (NCBI) 16, 175
RSP_2809 RSP_2809 ABC transporter, inner membrane subunit (NCBI) 4, 184
RSP_2849 RSP_2849 hypothetical membrane protein (NCBI) 2, 4
RSP_2883 pgm Probable phosphoglucomutase/phosphomannomutase (NCBI) 175, 384
RSP_2885 glgA glycogen synthase (NCBI) 4, 96
RSP_2898 RSP_2898 putative DNA polymerase III chi subunit (NCBI) 4, 175
RSP_2899 RSP_2899 Probable cytosol aminopeptidase (NCBI) 4, 175
RSP_3246 RSP_3246 putative D-alanyl-D-alanine carboxypeptidase (NCBI) 175, 384
RSP_3381 RSP_3381 NAD(P)H -dependent quinone oxidoreductase (NCBI) 57, 175
RSP_3419 RSP_3419 hypothetical protein (NCBI) 175, 381
RSP_3452 RSP_3452 TRAP-T family transporter, small (4TMs) inner membrane subunit (NCBI) 4, 61
RSP_3453 RSP_3453 TRAP-T family transporter, periplasmic binding protein (NCBI) 4, 61
RSP_3759 RSP_3759 Putative endonuclease (NCBI) 130, 175
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_2898
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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