Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_4345

tRNA-Glu (NCBI)

CircVis
Functional Annotations (1)
Function System
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_4345
(Mouseover regulator name to see its description)

RSP_4345 is regulated by 17 influences and regulates 0 modules.
Regulators for RSP_4345 (17)
Regulator Module Operator
RSP_0402 34 tf
RSP_0443 34 tf
RSP_0601 34 tf
RSP_0755 34 tf
RSP_1032 34 tf
RSP_1871 34 tf
RSP_1890 34 tf
RSP_2346 34 tf
RSP_2591 34 tf
RSP_3029 34 tf
RSP_3094 34 tf
RSP_3341 34 tf
RSP_1231 246 tf
RSP_2867 246 tf
RSP_3464 246 tf
RSP_3684 246 tf
RSP_3700 246 tf

Warning: RSP_4345 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
7788 1.50e+02 AacA..cCtTcTAa..aaTt.AA
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7789 2.80e+01 AtcCTGaCgaAgc
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8210 3.60e-01 cgcCatcacgTtcat
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8211 9.20e+03 ATcgAacTGttcgC
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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_4345

RSP_4345 is enriched for 1 functions in 4 categories.
Enrichment Table (1)
Function System
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
Module neighborhood information for RSP_4345

RSP_4345 has total of 41 gene neighbors in modules 34, 246
Gene neighbors (41)
Gene Common Name Description Module membership
RSP_0028 RSP_0028 Putative short-chain dehydrogenase/reductase (NCBI) 246, 251
RSP_0522 RSP_0522 putative oxidoreductase (NCBI) 217, 246
RSP_0835 manB phosphomannomutase (NCBI) 153, 246
RSP_1115 RSP_1115 hypothetical protein (NCBI) 246, 292
RSP_1116 RSP_1116 glycosyltransferase (NCBI) 196, 246
RSP_1117 RSP_1117 hypothetical protein (NCBI) 137, 246
RSP_1118 RSP_1118 group 1 glycosyltransferase (NCBI) 246, 292
RSP_1119 RSP_1119 ABC protein exporter, fused ATPase and inner membrane subunits (NCBI) 196, 246
RSP_1120 RSP_1120 protein secretion protein, HlyD family, membrane fusion protein (NCBI) 137, 246
RSP_1284 prkA Phosphoribulokinase (NCBI) 34, 284
RSP_1285 cbbF1 Fructose-1,6-bisphosphatase I (NCBI) 34, 284
RSP_1302 motB putative chemotaxis MotB protein (NCBI) 31, 246
RSP_1303 flgE putative flagellar hook protein (NCBI) 29, 246
RSP_1304 RSP_1304 putative flagellar hook protein (NCBI) 124, 246
RSP_1305 RSP_1305 putative flagellar hook-associated protein (NCBI) 138, 246
RSP_1307 flgI putative flagellar P-ring protein (NCBI) 31, 246
RSP_1630 RSP_1630 hypothetical protein (NCBI) 31, 246
RSP_2757 RSP_2757 hypothetical protein (NCBI) 236, 246
RSP_2758 RSP_2758 hypothetical protein (NCBI) 246, 251
RSP_2759 RSP_2759 hypothetical protein (NCBI) 246, 282
RSP_2760 RSP_2760 hypothetical protein (NCBI) 246, 251
RSP_2761 RSP_2761 putative P2-like prophage tail protein X (NCBI) 246, 282
RSP_3108 RSP_3108 Putative methyl accepting chemotaxis protein (NCBI) 246, 292
RSP_3116 RSP_3116 Conserved hypothetical membrane/transport protein (NCBI) 246, 370
RSP_3266 fbpB fructose-1,6-bisphosphatase (NCBI) 34, 284
RSP_3267 prkB Phosphoribulokinase (NCBI) 34, 284
RSP_3268 tklB Transketolase (NCBI) 34, 284
RSP_3269 gapB Glyceraldehyde 3-phosphate dehydrogenase (NCBI) 34, 284
RSP_3270 cfxB Fructose-bisphosphate aldolase II (NCBI) 34, 284
RSP_3271 rbpL Ribulose bisphosphate carboxylase, large chain, form II (NCBI) 34, 284
RSP_3284 iolD Acetolactate synthase (NCBI) 176, 246
RSP_3285 iolE possible sugar phosphate isomerases/epimerases, IolE (NCBI) 150, 246
RSP_3286 iolB Uncharacterized enzyme involved in inositol metabolism, IolB (NCBI) 246, 380
RSP_3630 RSP_3630 hypothetical protein (NCBI) 246, 253
RSP_3811 RSP_3811 hypothetical protein (NCBI) 138, 246
RSP_4326 RSP_4326 tRNA-Leu (NCBI) 34, 257
RSP_4345 RSP_4345 tRNA-Glu (NCBI) 34, 246
RSP_6081 RSP_6081 hypothetical protein (NCBI) 34, 284
RSP_6168 RSP_6168 ABC Cobalt transporter, periplasmic binding protein CbiN (NCBI) 34, 241
RSP_6189 RSP_6189 hypothetical protein (NCBI) 34, 230
RSP_6245 RSP_6245 hypothetical protein (NCBI) 8, 34
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_4345
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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