Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2004 trpE

Anthranilate synthase component I and chorismate binding protein (NCBI)

CircVis
Functional Annotations (8)
Function System
Anthranilate/para-aminobenzoate synthases component I cog/ cog
tryptophan biosynthetic process go/ biological_process
anthranilate synthase activity go/ molecular_function
anthranilate synthase complex go/ cellular_component
Phenylalanine tyrosine and tryptophan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
trpE_most tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2004
(Mouseover regulator name to see its description)

RSP_2004 is regulated by 24 influences and regulates 0 modules.
Regulators for RSP_2004 trpE (24)
Regulator Module Operator
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
RSP_0774 268 tf
RSP_0907 268 tf
RSP_1163 268 tf
RSP_1191 268 tf
RSP_1231 268 tf
RSP_1739 268 tf
RSP_1741 268 tf
RSP_3124 268 tf
RSP_3179 268 tf
RSP_3309 268 tf
RSP_3664 268 tf
RSP_3676 268 tf
RSP_3686 268 tf

Warning: RSP_2004 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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8254 7.30e+01 GCccTgTCatTtG
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8255 2.80e+03 AAaCTGacaT
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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_2004

RSP_2004 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Anthranilate/para-aminobenzoate synthases component I cog/ cog
tryptophan biosynthetic process go/ biological_process
anthranilate synthase activity go/ molecular_function
anthranilate synthase complex go/ cellular_component
Phenylalanine tyrosine and tryptophan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
trpE_most tigr/ tigrfam
Module neighborhood information for RSP_2004

RSP_2004 has total of 47 gene neighbors in modules 203, 268
Gene neighbors (47)
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_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_0780 RSP_0780 hypothetical protein with ATP/GTP-binding site (NCBI) 13, 268
RSP_0829 lctB Lactate dehydrogenase (NCBI) 148, 203
RSP_0848 xthA1 Exodeoxyribonuclease III (NCBI) 184, 268
RSP_0862 leuD 3-isopropylmalate dehydratase small subunit (NCBI) 203, 277
RSP_0863 leuC 3-isopropylmalate dehydratase large subunit (NCBI) 30, 203
RSP_0944 purU PurU, Formyltetrahydrofolate deformylase (NCBI) 124, 268
RSP_0998 nhaD Na+/H+ antiporter, NhaD (NCBI) 160, 268
RSP_1052 RSP_1052 possible Acetyltransferase (NCBI) 268, 271
RSP_1105 DapB Dihydrodipicolinate reductase (DHPR) (NCBI) 268, 299
RSP_1381 RSP_1381 hypothetical protein (NCBI) 47, 268
RSP_1382 RSP_1382 radical SAM superfamily protein (NCBI) 266, 268
RSP_1484 RSP_1484 hypothetical protein (NCBI) 209, 268
RSP_1485 RSP_1485 ATP-dependent RNA helicase (NCBI) 209, 268
RSP_1706 RSP_1706 Putative acetyltransferase (NCBI) 13, 268
RSP_1735 secY Preprotein translocase SecY subunit (NCBI) 203, 224
RSP_1766 pykA Pyruvate kinase (NCBI) 203, 301
RSP_1832 RSP_1832 peptidase, M16 family (NCBI) 69, 268
RSP_1989 valS Putative valyl-tRNA synthetase (NCBI) 160, 203
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_2304 ribF Riboflavin kinase / FAD synthetase = FMN adenylyltransferase, RibF (NCBI) 268, 343
RSP_2454 purF Amidophosphoribosyltransferase (NCBI) 218, 268
RSP_2465 RSP_2465 hypothetical protein (NCBI) 25, 203
RSP_2714 lpxA Acyl-(acyl carrier protein))-UDP-N-acetylglucosamine O-acyltransferase (NCBI) 268, 281
RSP_2778 RSP_2778 hypothetical protein (NCBI) 224, 268
RSP_2841 trkA potassium uptake tranporter, NAD-binding subunit, TrkA (NCBI) 63, 268
RSP_2887 glgP glycogen phosphorylase (NCBI) 203, 261
RSP_2902 RSP_2902 Putative organic solvent tolerance protein (NCBI) 87, 268
RSP_2951 purL FGAM synthase synthetase domain (NCBI) 203, 258
RSP_3080 RSP_3080 Choline/carnitine/betaine transporter, BCCT family (NCBI) 160, 203
RSP_3549 hisG ATP phosphoribosyltransferase (NCBI) 160, 268
RSP_3550 RSP_3550 Aminoacyl-transfer RNA synthetase, class II (NCBI) 212, 268
RSP_3592 aroA EPSP synthase, 3-phosphoshikimate 1-carboxyvinyltransferase (NCBI) 203, 323
RSP_3664 RSP_3664 transcriptional regulator, GntR family (NCBI) 268, 331
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.

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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.

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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.
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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