Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0957 pyrD

Probable dihydroorotate dehydrogenase (NCBI)

CircVis
Functional Annotations (9)
Function System
Dihydroorotate dehydrogenase cog/ cog
dihydroorotate dehydrogenase activity go/ molecular_function
dihydroorotate oxidase activity go/ molecular_function
'de novo' pyrimidine base biosynthetic process go/ biological_process
UMP biosynthetic process go/ biological_process
membrane go/ cellular_component
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
pyrD_sub2 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0957
(Mouseover regulator name to see its description)

RSP_0957 is regulated by 24 influences and regulates 0 modules.
Regulators for RSP_0957 pyrD (24)
Regulator Module Operator
RSP_0068 293 tf
RSP_0090 293 tf
RSP_0327 293 tf
RSP_0623 293 tf
RSP_0722 293 tf
RSP_0755 293 tf
RSP_1590 293 tf
RSP_2200 293 tf
RSP_2533 293 tf
RSP_2838 293 tf
RSP_2850 293 tf
RSP_3324 293 tf
RSP_0395 375 tf
RSP_0794 375 tf
RSP_0927 375 tf
RSP_1164 375 tf
RSP_1435 375 tf
RSP_1663 375 tf
RSP_1945 375 tf
RSP_2922 375 tf
RSP_3309 375 tf
RSP_3616 375 tf
RSP_3664 375 tf
RSP_3665 375 tf

Warning: RSP_0957 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
8300 1.30e+00 aAaatTgtaACcttgcatgGa
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8301 1.40e+04 GAtGtTGAGGcAGgT
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8442 1.10e+03 AGATTT
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8443 4.10e+03 aaAcgcCcGC.c.cTgt...AGG
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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_0957

RSP_0957 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Dihydroorotate dehydrogenase cog/ cog
dihydroorotate dehydrogenase activity go/ molecular_function
dihydroorotate oxidase activity go/ molecular_function
'de novo' pyrimidine base biosynthetic process go/ biological_process
UMP biosynthetic process go/ biological_process
membrane go/ cellular_component
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
pyrD_sub2 tigr/ tigrfam
Module neighborhood information for RSP_0957

RSP_0957 has total of 30 gene neighbors in modules 293, 375
Gene neighbors (30)
Gene Common Name Description Module membership
RSP_0349 RSP_0349 ABC transporter, ATPase subunit (NCBI) 267, 293
RSP_0376 RSP_0376 Glutamine amidotransferase class-I (NCBI) 273, 375
RSP_0420 RSP_0420 hypothetical protein (NCBI) 121, 293
RSP_0449 RSP_0449 putative glutamine amidotransferase (NCBI) 20, 293
RSP_0450 RSP_0450 hypothetical protein (NCBI) 293, 326
RSP_0594 RSP_0594 Putative choline sulfatase (NCBI) 265, 293
RSP_0656 RSP_0656 Probable sodium/sulphate symporter (NCBI) 130, 293
RSP_0854 RSP_0854 Predicted ornithine cyclodeaminase (NCBI) 16, 293
RSP_0928 RSP_0928 hypothetical protein (NCBI) 53, 375
RSP_0956 RSP_0956 hypothetical protein (NCBI) 354, 375
RSP_0957 pyrD Probable dihydroorotate dehydrogenase (NCBI) 293, 375
RSP_1213 RSP_1213 hypothetical protein (NCBI) 157, 293
RSP_1422 RSP_1422 ParB-like nuclease (NCBI) 259, 293
RSP_1423 RSP_1423 ParA family ATPase (NCBI) 68, 293
RSP_1483 RSP_1483 hypothetical protein (NCBI) 240, 293
RSP_1800 RSP_1800 hypothetical protein (NCBI) 234, 293
RSP_1930 pyrC Dihydroorotase, homodimeric type (NCBI) 256, 375
RSP_1983 sqdA Phospholipid/glycerol acyltransferase (NCBI) 293, 384
RSP_2316 dadA D-amino acid dehydrogenase (NCBI) 68, 375
RSP_2348 RSP_2348 hypothetical protein (NCBI) 68, 293
RSP_2349 RSP_2349 hypothetical protein (NCBI) 293, 355
RSP_2350 RSP_2350 hypothetical protein (NCBI) 112, 293
RSP_2495 nrd putative class II ribonucleoside-diphosphate reductase (NCBI) 293, 326
RSP_2832 RSP_2832 Predicted conserved flavoprotein (NCBI) 53, 375
RSP_2842 trkH1 potassium uptake transporter, transmembrane subunit, TrkH (NCBI) 174, 293
RSP_3308 RSP_3308 possible transporter, DME family, DMT superfamily (NCBI) 133, 375
RSP_3330 sac1 Putative sodium/sulfate transporter, DASS family (NCBI) 67, 375
RSP_3350 RSP_3350 Lipocalin-related protein (NCBI) 107, 293
RSP_3513 RSP_3513 GAF sensor diguanylate cyclase (NCBI) 57, 293
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_0957
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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