Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0712 recR

recombination protein RecR (NCBI)

CircVis
Functional Annotations (7)
Function System
Recombinational DNA repair protein (RecF pathway) cog/ cog
nucleic acid binding go/ molecular_function
DNA repair go/ biological_process
DNA modification go/ biological_process
DNA recombination go/ biological_process
Homologous recombination kegg/ kegg pathway
recR tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0712
(Mouseover regulator name to see its description)

RSP_0712 is regulated by 22 influences and regulates 0 modules.
Regulators for RSP_0712 recR (22)
Regulator Module Operator
RSP_1607 173 tf
RSP_1871 173 tf
RSP_2610 173 tf
RSP_2800 173 tf
RSP_2867 173 tf
RSP_2963 173 tf
RSP_3238 173 tf
RSP_3322 173 tf
RSP_0071 358 tf
RSP_0090 358 tf
RSP_0282 358 tf
RSP_0394 358 tf
RSP_0443 358 tf
RSP_0601 358 tf
RSP_0698 358 tf
RSP_1243 358 tf
RSP_1590 358 tf
RSP_1871 358 tf
RSP_2410 358 tf
RSP_2888 358 tf
RSP_2965 358 tf
RSP_3505 358 tf

Warning: RSP_0712 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
8066 3.60e+00 cCgGTTAagactGCggCCgcaTGC
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8067 2.10e+01 aa.GTG.gGcAagaaccggaaAAC
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8414 2.30e-01 AtcCccTtttcagCtTctt
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8415 1.60e+02 at.t.gAtgtaggt.aAg..att
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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_0712

RSP_0712 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Recombinational DNA repair protein (RecF pathway) cog/ cog
nucleic acid binding go/ molecular_function
DNA repair go/ biological_process
DNA modification go/ biological_process
DNA recombination go/ biological_process
Homologous recombination kegg/ kegg pathway
recR tigr/ tigrfam
Module neighborhood information for RSP_0712

RSP_0712 has total of 46 gene neighbors in modules 173, 358
Gene neighbors (46)
Gene Common Name Description Module membership
RSP_0015 RSP_0015 ABC spermidine/putrescine transporter, ATPase subunit (NCBI) 221, 358
RSP_0090 smoC Operon regulator SmoC (NCBI) 99, 358
RSP_0111N RSP_0111N None 49, 358
RSP_0223 RSP_0223 hypothetical protein (NCBI) 93, 358
RSP_0224 RSP_0224 ATP-dependent helicase (NCBI) 93, 358
RSP_0282 ppsR Transcriptional regulator, PpsR (NCBI) 358, 381
RSP_0468 RSP_0468 putative 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (NCBI) 275, 358
RSP_0582 RSP_0582 possible penicillin binding protein (NCBI) 118, 358
RSP_0710 dnaX DNA polymerase III tau and gamma subunits (NCBI) 173, 381
RSP_0711 YbaB hypothetical protein (NCBI) 173, 187
RSP_0712 recR recombination protein RecR (NCBI) 173, 358
RSP_0731 RSP_0731 hypothetical protein (NCBI) 173, 261
RSP_0732 RSP_0732 hypothetical protein (NCBI) 173, 261
RSP_0733 RSP_0733 cell division ATP-binding protein FtsE (NCBI) 173, 261
RSP_0734 RSP_0734 cell division protein FtsX (NCBI) 173, 261
RSP_0735 RSP_0735 Phospholipid/glycerol acyltransferase (NCBI) 173, 261
RSP_0811 RSP_0811 hypothetical protein (NCBI) 173, 207
RSP_0812 RSP_0812 Glyoxalase I (lactoylglutathione lyase) (NCBI) 108, 173
RSP_0889 glnK Nitrogen regulatory protein P-II (NCBI) 57, 358
RSP_1232 RSP_1232 putative integral membrane protein (NCBI) 108, 173
RSP_1478 RSP_1478 ABC oligopeptide transporter, fused ATPase subunits (NCBI) 173, 305
RSP_1479 OppC ABC oligopeptide transporter, inner membrane subunit OppC (NCBI) 173, 305
RSP_1480 OppB ABC oligopeptide transporter, inner membrane subunit OppB (NCBI) 173, 305
RSP_1481 OppA ABC oligopeptide transporter, perplasmic substrate-binding protein OppA (NCBI) 173, 305
RSP_1565 appA AppA, antirepressor of ppsR, sensor of blue light (NCBI) 139, 358
RSP_1590 RSP_1590 two component, sigma54 specific, transcriptional regulator, fis family (NCBI) 175, 358
RSP_2042 RSP_2042 hypothetical protein (NCBI) 65, 358
RSP_2044 RSP_2044 ATPase (NCBI) 65, 358
RSP_2047 RSP_2047 ThiF family protein (NCBI) 100, 358
RSP_2048 RSP_2048 hypothetical protein (NCBI) 100, 358
RSP_2210 RSP_2210 ABC sugar transporter, fused ATPase subunits (NCBI) 174, 358
RSP_2338 RSP_2338 hypothetical protein (NCBI) 358, 377
RSP_2415 RSP_2415 hypothetical protein (NCBI) 82, 358
RSP_2416 RSP_2416 hypothetical protein (NCBI) 82, 358
RSP_2417 RSP_2417 hypothetical protein (NCBI) 82, 358
RSP_3215 RSP_3215 hypothetical protein (NCBI) 176, 358
RSP_3585 RSP_3585 Tryptophan synthase beta chain (NCBI) 173, 182
RSP_3586 RSP_3586 Putative aromatic pathway regulator (NCBI) 36, 173
RSP_3587 RSP_3587 N-(5'-phosphoribosyl)anthranilate isomerase (NCBI) 173, 382
RSP_3750 RSP_3750 hypothetical protein (NCBI) 21, 358
RSP_3751 RSP_3751 hypothetical protein (NCBI) 21, 358
RSP_3752 RSP_3752 hypothetical protein (NCBI) 21, 358
RSP_3755 RSP_3755 hypothetical protein (NCBI) 21, 358
RSP_3756 RSP_3756 hypothetical protein (NCBI) 21, 358
RSP_3757 RSP_3757 hypothetical protein (NCBI) 21, 358
RSP_4355 RSP_4355 hypothetical protein (NCBI) 24, 173
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_0712
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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