Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2705 pyrH

Uridylate kinase (NCBI)

CircVis
Functional Annotations (7)
Function System
Uridylate kinase cog/ cog
pyrimidine nucleotide biosynthetic process go/ biological_process
cellular amino acid biosynthetic process go/ biological_process
uridylate kinase activity go/ molecular_function
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
pyrH_bact tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2705
(Mouseover regulator name to see its description)

RSP_2705 is regulated by 19 influences and regulates 0 modules.
Regulators for RSP_2705 pyrH (19)
Regulator Module Operator
RSP_0728 360 tf
RSP_1014 360 tf
RSP_1077 360 tf
RSP_1231 360 tf
RSP_1704 360 tf
RSP_1925 360 tf
RSP_2130 360 tf
RSP_2494 360 tf
RSP_2610 360 tf
RSP_3684 360 tf
RSP_3700 360 tf
RSP_0395 109 tf
RSP_0728 109 tf
RSP_1231 109 tf
RSP_1739 109 tf
RSP_2494 109 tf
RSP_2572 109 tf
RSP_2730 109 tf
RSP_3309 109 tf

Warning: RSP_2705 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
7938 1.50e+01 GtTTTCGGacatTT
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7939 3.20e+04 GAactGaAaccttgcCttCcgcC
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8418 4.10e-02 tTttggCaaGAtcgc
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8419 5.00e+02 AAATtCAA
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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_2705

RSP_2705 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Uridylate kinase cog/ cog
pyrimidine nucleotide biosynthetic process go/ biological_process
cellular amino acid biosynthetic process go/ biological_process
uridylate kinase activity go/ molecular_function
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
pyrH_bact tigr/ tigrfam
Module neighborhood information for RSP_2705

RSP_2705 has total of 45 gene neighbors in modules 109, 360
Gene neighbors (45)
Gene Common Name Description Module membership
RSP_0142 RSP_0142 FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) (NCBI) 109, 369
RSP_0367 RSP_0367 Preprotein translocase SecG subunit (NCBI) 203, 360
RSP_0385 RSP_0385 Threonyl-tRNA synthetase, class IIa (NCBI) 166, 360
RSP_0403 RSP_0403 homoserine dehydrogenase (NCBI) 109, 299
RSP_0444 RSP_0444 hypothetical protein (NCBI) 43, 360
RSP_0584 RSP_0584 Lysyl-tRNA synthetase (NCBI) 109, 279
RSP_0587 RSP_0587 Putative ABC transporter, fused ATPase subunits (NCBI) 109, 360
RSP_0655 RSP_0655 hypothetical protein (NCBI) 109, 369
RSP_0714 RSP_0714 hypothetical protein (NCBI) 109, 277
RSP_0929 accD Acetyl-CoA carboxylase carboxyl transferase, beta subunit (NCBI) 309, 360
RSP_1068 argB acetylglutamate kinase (NCBI) 109, 192
RSP_1153 GutQ Sugar phosphate Isomerase (NCBI) 109, 192
RSP_1161 RSP_1161 3'-Phosphadenosine 5'-phosphosulfate 3'-phosphatase (NCBI) 109, 384
RSP_1212 argG ArgG, Argininosuccinate synthase (NCBI) 109, 166
RSP_1351 serC phosphoserine aminotransferase (NCBI) 85, 360
RSP_1352 RSP_1352 D-3-phosphoglycerate dehydrogenase (NCBI) 85, 360
RSP_1494 RSP_1494 putative aspartate aminotransferase (NCBI) 349, 360
RSP_1495 RSP_1495 Putative cell division protein (NCBI) 349, 360
RSP_1514 ahcY Adenosylhomocysteinase (NCBI) 299, 360
RSP_1519 prrC PrrC (NCBI) 43, 360
RSP_1575 sopT sulfate adenylyltransferase (NCBI) 109, 271
RSP_1674 RSP_1674 type 1 signal peptidase (NCBI) 224, 360
RSP_1763 pheS Phenylalanyl-tRNA synthetase alpha subunit (NCBI) 109, 360
RSP_1795 serS Probable Seryl-tRNA synthetase (NCBI) 109, 192
RSP_1808 trpS tryptophanyl-tRNA synthetase (NCBI) 71, 360
RSP_1831 thrC Threonine synthase (NCBI) 109, 192
RSP_1849 RSP_1849 Aspartate kinase (NCBI) 109, 271
RSP_1851 metZ O-succinylhomoserine sulfhydrylase (NCBI) 71, 360
RSP_1856 glyQ Heterodimeric glycyl-transfer RNA synthetase (NCBI) 109, 258
RSP_2126 purC SAICAR synthetase (NCBI) 261, 360
RSP_2221 purB Adenylosuccinate lyase (NCBI) 109, 369
RSP_2258 purC SAICAR synthetase (NCBI) 43, 109
RSP_2301 prsA Phosphoribosyl pyrophosphate synthetase (NCBI) 109, 203
RSP_2307 RSP_2307 probable manganese-dependent inorganic pyrophosphatase (NCBI) 109, 166
RSP_2455 RSP_2455 putative Colicin V production protein, dedE (NCBI) 109, 299
RSP_2543 RSP_2543 Peptidoglycan-binding LysM (possible peptidase) (NCBI) 261, 360
RSP_2615 RSP_2615 hypothetical protein (NCBI) 109, 345
RSP_2705 pyrH Uridylate kinase (NCBI) 109, 360
RSP_2706 frr Ribosome recycling factor (NCBI) 109, 360
RSP_2710 RSP_2710 Putative membrane-associated zinc metalloprotease (NCBI) 36, 360
RSP_2711 RSP_2711 putative outer membrane protein (NCBI) 43, 360
RSP_2956 tktA Transketolase (NCBI) 166, 360
RSP_2959 gapB Glyceraldehyde 3-phosphate dehydrogenase B (GAPDH) (NCBI) 184, 360
RSP_3177 fabB 3-oxoacyl-(Acyl-carrier-protein) synthase (NCBI) 360, 363
RSP_3178 fabA 3-hydroxydecanoyl-(acyl-carrier-protein) dehydratase (NCBI) 360, 363
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_2705
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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