Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2537 prfC

Probable peptide chain release factor RF3 (NCBI)

CircVis
Functional Annotations (7)
Function System
Peptide chain release factor RF-3 cog/ cog
GTPase activity go/ molecular_function
GTP binding go/ molecular_function
cytoplasm go/ cellular_component
translational termination go/ biological_process
translation release factor activity, codon specific go/ molecular_function
small_GTP tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2537
(Mouseover regulator name to see its description)

RSP_2537 is regulated by 23 influences and regulates 0 modules.
Regulators for RSP_2537 prfC (23)
Regulator Module Operator
RSP_0394 72 tf
RSP_1231 72 tf
RSP_1776 72 tf
RSP_2346 72 tf
RSP_2533 72 tf
RSP_2840 72 tf
RSP_2889 72 tf
RSP_2922 72 tf
RSP_3001 72 tf
RSP_3680 72 tf
RSP_0394 166 tf
RSP_0395 166 tf
RSP_0698 166 tf
RSP_0755 166 tf
RSP_1163 166 tf
RSP_1231 166 tf
RSP_1704 166 tf
RSP_1739 166 tf
RSP_2494 166 tf
RSP_2730 166 tf
RSP_2850 166 tf
RSP_2889 166 tf
RSP_2922 166 tf

Warning: RSP_2537 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
7864 3.50e-07 AtagggCcg.ATCctcttgCcCTT
Loader icon
7865 5.20e-05 AcTCaaGaAcAacACaAGccAAAC
Loader icon
8052 4.30e+00 TTtccCGC
Loader icon
8053 4.70e+02 AATTCAGACCTTTTCCTGA
Loader icon
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_2537

RSP_2537 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Peptide chain release factor RF-3 cog/ cog
GTPase activity go/ molecular_function
GTP binding go/ molecular_function
cytoplasm go/ cellular_component
translational termination go/ biological_process
translation release factor activity, codon specific go/ molecular_function
small_GTP tigr/ tigrfam
Module neighborhood information for RSP_2537

RSP_2537 has total of 46 gene neighbors in modules 72, 166
Gene neighbors (46)
Gene Common Name Description Module membership
RSP_0005 guaA GMP synthase (glutamine-hydrolyzing) (NCBI) 166, 258
RSP_0385 RSP_0385 Threonyl-tRNA synthetase, class IIa (NCBI) 166, 360
RSP_0404 RSP_0404 fructose - 1,6 - bisphosphatase, GlpX-like (NCBI) 166, 203
RSP_0657 RSP_0657 hypothetical protein (NCBI) 30, 72
RSP_0658 RSP_0658 Probable ATP-dependent helicase (NCBI) 30, 72
RSP_0659 RSP_0659 Putative metallo-phosphoesterase (NCBI) 30, 72
RSP_0778 ProS Prolyl-tRNA synthetase, class IIa (NCBI) 166, 258
RSP_0815 aspS Aspartyl-tRNA synthetase (NCBI) 166, 248
RSP_0821 RSP_0821 Esterase/lipase/thioesterase (NCBI) 72, 356
RSP_0827 RSP_0827 Ribosomal protein L25 (NCBI) 104, 166
RSP_0832 RSP_0832 Putative GTP-binding protein (NCBI) 166, 192
RSP_0968 mdh malate dehydrogenase (RefSeq) 25, 166
RSP_1086 sdh saccharopine dehydrogenase (NAD+, L-lysine forming) (NCBI) 72, 175
RSP_1160 kdsB CMP-2-keto-3-deoxyoctulaosonic acid synthetase (NCBI) 72, 184
RSP_1212 argG ArgG, Argininosuccinate synthase (NCBI) 109, 166
RSP_1375 RSP_1375 hypothetical protein (NCBI) 72, 278
RSP_1376 asd putative aspartate-semialdehyde dehydrogenase (NCBI) 166, 192
RSP_1754 RSP_1754 hypothetical protein (NCBI) 72, 384
RSP_1761 pheT Phenylalanyl-tRNA synthetase beta chain (NCBI) 51, 166
RSP_1908 RSP_1908 outer membrane protein, OmpA/MotB family (NCBI) 72, 381
RSP_2088 lepA GTP-binding elongation factor (NCBI) 51, 166
RSP_2267 RSP_2267 hypothetical protein (NCBI) 39, 72
RSP_2307 RSP_2307 probable manganese-dependent inorganic pyrophosphatase (NCBI) 109, 166
RSP_2332 RSP_2332 hypothetical protein (NCBI) 67, 72
RSP_2333 nadE NH3 dependent NAD synthetase, NadE (NCBI) 72, 299
RSP_2341 RSP_2341 putative aminotransferase protein / Aspartate aminotransferase (2.6.1.1) (NCBI) 72, 343
RSP_2343 RSP_2343 Putative threonine efflux protein, RhtB family (NCBI) 72, 343
RSP_2344 fabI1 enoyl-acyl carrier protein reductase (NCBI) 72, 200
RSP_2345 pdxH Pyridoxamine 5'-phosphate oxidase (NCBI) 72, 343
RSP_2453 RSP_2453 putative oxidoreductase (NAD/NADP dependent) (NCBI) 71, 166
RSP_2461 fabG 3-oxoacyl-(acyl-carrier protein) reductase (NCBI) 166, 195
RSP_2537 prfC Probable peptide chain release factor RF3 (NCBI) 72, 166
RSP_2544 RSP_2544 Protein-L-isoaspartate O-methyltransferase (NCBI) 7, 72
RSP_2545 surE Survival protein SurE (NCBI) 39, 72
RSP_2697 RSP_2697 hypothetical protein (NCBI) 166, 184
RSP_2698 RSP_2698 putative quinoprotein (NCBI) 166, 240
RSP_2699 RSP_2699 Probable GTP-binding protein (NCBI) 166, 271
RSP_2737 RSP_2737 Putative ssRNA endoribonuclease L-PSP (NCBI) 166, 345
RSP_2956 tktA Transketolase (NCBI) 166, 360
RSP_3072 sndh putative L-sorbosone dehydrogenase (NCBI) 23, 72
RSP_3349 RSP_3349 hypothetical protein (NCBI) 133, 166
RSP_3771 RSP_3771 hypothetical protein (NCBI) 72, 213
RSP_4042 RSP_4042 Peptidyl-prolyl cis-trans isomerase, cyclophilin type (NCBI) 166, 345
RSP_4043 RSP_4043 Peptidylprolyl isomerase (NCBI) 162, 166
RSP_4044 pgk Phosphoglycerate kinase (NCBI) 166, 299
RSP_4045 fbaB Fructose-bisphosphate aldolase class I (NCBI) 166, 299
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_2537
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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