Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0756 ribH1

6,7-dimethyl-8-ribityllumazine synthase beta chain (NCBI)

CircVis
Functional Annotations (7)
Function System
Riboflavin synthase beta-chain cog/ cog
riboflavin synthase activity go/ molecular_function
riboflavin biosynthetic process go/ biological_process
riboflavin synthase complex go/ cellular_component
Riboflavin metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
lumazine-synth tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0756
(Mouseover regulator name to see its description)

RSP_0756 is regulated by 25 influences and regulates 0 modules.
Regulators for RSP_0756 ribH1 (25)
Regulator Module Operator
RSP_0395 279 tf
RSP_0443 279 tf
RSP_0489 279 tf
RSP_0511 279 tf
RSP_0527 279 tf
RSP_1163 279 tf
RSP_1191 279 tf
RSP_1231 279 tf
RSP_1922 279 tf
RSP_2324 279 tf
RSP_2730 279 tf
RSP_2850 279 tf
RSP_3022 279 tf
RSP_3616 279 tf
RSP_0394 203 tf
RSP_0395 203 tf
RSP_0728 203 tf
RSP_1231 203 tf
RSP_1739 203 tf
RSP_2494 203 tf
RSP_2533 203 tf
RSP_2850 203 tf
RSP_3095 203 tf
RSP_3616 203 tf
RSP_3680 203 tf

Warning: RSP_0756 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
8126 5.30e+03 GACGAcatTT
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8127 1.20e+04 ATAAAA
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8272 4.40e-07 CCTcTGcaaGgCGacttcTCaaG
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8273 1.90e+00 AaAcAGGA.CG
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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_0756

RSP_0756 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Riboflavin synthase beta-chain cog/ cog
riboflavin synthase activity go/ molecular_function
riboflavin biosynthetic process go/ biological_process
riboflavin synthase complex go/ cellular_component
Riboflavin metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
lumazine-synth tigr/ tigrfam
Module neighborhood information for RSP_0756

RSP_0756 has total of 52 gene neighbors in modules 203, 279
Gene neighbors (52)
Gene Common Name Description Module membership
RSP_0029 RSP_0029 acetyl-CoA hydrolase/transferase family protein (NCBI) 203, 261
RSP_0239 PntB Pyridine nucleotide transhydrogenase beta subunit (NCBI) 15, 203
RSP_0240 pntA Pyridine nucleotide transhydrogenase alpha subunit (NCBI) 15, 203
RSP_0248 RSP_0248 elongation factor EF-P (NCBI) 203, 311
RSP_0367 RSP_0367 Preprotein translocase SecG subunit (NCBI) 203, 360
RSP_0404 RSP_0404 fructose - 1,6 - bisphosphatase, GlpX-like (NCBI) 166, 203
RSP_0446 RSP_0446 Isocitrate dehydrogenase (NCBI) 279, 297
RSP_0561 RSP_0561 Transaldolase (NCBI) 279, 349
RSP_0562 RSP_0562 hypothetical protein (NCBI) 54, 279
RSP_0584 RSP_0584 Lysyl-tRNA synthetase (NCBI) 109, 279
RSP_0675 RSP_0675 putative TatD-related deoxyribonuclease (NCBI) 182, 203
RSP_0719 RSP_0719 Phosphatidylserine decarboxylase (NCBI) 203, 306
RSP_0720 pssA CDP-alcohol phosphatidyltransferase (NCBI) 203, 306
RSP_0756 ribH1 6,7-dimethyl-8-ribityllumazine synthase beta chain (NCBI) 203, 279
RSP_0757 ribBA Bifunctional GTP cyclohydrolase II/3,4-dihydroxy-2butanone-4-phosphate synthase (NCBI) 203, 279
RSP_0829 lctB Lactate dehydrogenase (NCBI) 148, 203
RSP_0862 leuD 3-isopropylmalate dehydratase small subunit (NCBI) 203, 277
RSP_0863 leuC 3-isopropylmalate dehydratase large subunit (NCBI) 30, 203
RSP_0873 RSP_0873 N-formylmethionyl tRNA deformylase (NCBI) 279, 306
RSP_0883 RSP_0883 SmpB protein (NCBI) 277, 279
RSP_1045 trmD tRNA (guanine-N1-)-methyltransferase (NCBI) 279, 356
RSP_1350 serB phosphoserine phosphatase (NCBI) 258, 279
RSP_1459 RSP_1459 hypothetical protein (NCBI) 93, 279
RSP_1461 kdtA Putative 3-deoxy-D-manno-octulosonic-acid transferase (NCBI) 184, 279
RSP_1735 secY Preprotein translocase SecY subunit (NCBI) 203, 224
RSP_1766 pykA Pyruvate kinase (NCBI) 203, 301
RSP_1806 RSP_1806 aconitate hydratase (RefSeq) 279, 297
RSP_1989 valS Putative valyl-tRNA synthetase (NCBI) 160, 203
RSP_1994 gltA Citrate synthase (NCBI) 279, 309
RSP_2004 trpE Anthranilate synthase component I and chorismate binding protein (NCBI) 203, 268
RSP_2005 ybaU possible peptidyl-prolyl cis-trans isomerse (NCBI) 203, 323
RSP_2296 atpH ATPase, delta (OSCP) subunit (NCBI) 203, 369
RSP_2301 prsA Phosphoribosyl pyrophosphate synthetase (NCBI) 109, 203
RSP_2306 RSP_2306 putative HAD superfamily protein (NCBI) 234, 279
RSP_2465 RSP_2465 hypothetical protein (NCBI) 25, 203
RSP_2845 RSP_2845 putative penicillin acylase (penicillin amidase) (NCBI) 195, 279
RSP_2887 glgP glycogen phosphorylase (NCBI) 203, 261
RSP_2910 RSP_2910 Predicted Metal-dependent amidase/aminoacylase/carboxypeptidase (NCBI) 98, 279
RSP_2912 RSP_2912 Predicted pyrophosphatase (NCBI) 279, 356
RSP_2951 purL FGAM synthase synthetase domain (NCBI) 203, 258
RSP_3080 RSP_3080 Choline/carnitine/betaine transporter, BCCT family (NCBI) 160, 203
RSP_3230 RSP_3230 hypothetical protein (NCBI) 103, 279
RSP_3231 RSP_3231 ABC peptide transporter, periplasmic binding protein (NCBI) 195, 279
RSP_3232 RSP_3232 ABC peptide transporter, inner membrane subunit (NCBI) 279, 297
RSP_3233 RSP_3233 ABC peptide transporter, inner membrane subunit (NCBI) 279, 297
RSP_3235 RSP_3235 ABC peptide transporter, ATPase subunit (NCBI) 279, 297
RSP_3236 RSP_3236 ABC peptide transporter, ATPase subunit (NCBI) 279, 297
RSP_3328 RSP_3328 hypothetical protein (NCBI) 279, 306
RSP_3592 aroA EPSP synthase, 3-phosphoshikimate 1-carboxyvinyltransferase (NCBI) 203, 323
RSP_3716 selD selenide, water dikinase (selenophosphate synthetase) (NCBI) 279, 311
RSP_3749 ampC putative beta-lactamase precursor (NCBI) 279, 362
RSP_3822 RSP_3822 GTP1/OBG family protein (NCBI) 30, 279
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_0756
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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