Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0716

NADPH/quinone reductase and related Zn-dependent oxidoreductases (NCBI)

CircVis
Functional Annotations (4)
Function System
NADPH:quinone reductase and related Zn-dependent oxidoreductases cog/ cog
zinc ion binding go/ molecular_function
oxidoreductase activity go/ molecular_function
quinone_pig3 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0716
(Mouseover regulator name to see its description)

RSP_0716 is regulated by 25 influences and regulates 0 modules.
Regulators for RSP_0716 (25)
Regulator Module Operator
RSP_0032 216 tf
RSP_0601 216 tf
RSP_0794 216 tf
RSP_0999 216 tf
RSP_1220 216 tf
RSP_2130 216 tf
RSP_2171 216 tf
RSP_2200 216 tf
RSP_2236 216 tf
RSP_2838 216 tf
RSP_3094 216 tf
RSP_3665 216 tf
RSP_3686 216 tf
RSP_0507 132 tf
RSP_0794 132 tf
RSP_1139 132 tf
RSP_1191 132 tf
RSP_1272 132 tf
RSP_1274 132 tf
RSP_1435 132 tf
RSP_2130 132 tf
RSP_2719 132 tf
RSP_2838 132 tf
RSP_2850 132 tf
RSP_3094 132 tf

Warning: RSP_0716 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
7984 7.40e-06 tATcAagTatTcTaAa
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7985 1.10e-04 aaaatTGttGCagcCAgG.aAagT
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8152 1.10e+00 aTcGA.aAG.T
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8153 3.90e+03 AtGATCaCGat
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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_0716

RSP_0716 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
NADPH:quinone reductase and related Zn-dependent oxidoreductases cog/ cog
zinc ion binding go/ molecular_function
oxidoreductase activity go/ molecular_function
quinone_pig3 tigr/ tigrfam
Module neighborhood information for RSP_0716

RSP_0716 has total of 52 gene neighbors in modules 132, 216
Gene neighbors (52)
Gene Common Name Description Module membership
RSP_0235 moaA molybdenum cofactor biosynthesis protein A (NCBI) 132, 368
RSP_0351 RSP_0351 D-threo-aldose 1-dehydrogenase (NCBI) 158, 216
RSP_0408 RSP_0408 hypothetical protein (NCBI) 134, 216
RSP_0424 RSP_0424 hypothetical protein (NCBI) 216, 285
RSP_0554 htpx heat shock protein--probable protease (NCBI) 132, 366
RSP_0559 msrA Peptide methionine sulfoxide reductase (NCBI) 134, 216
RSP_0608 RSP_0608 hypothetical protein (NCBI) 146, 216
RSP_0716 RSP_0716 NADPH/quinone reductase and related Zn-dependent oxidoreductases (NCBI) 132, 216
RSP_0870 RSP_0870 hypothetical protein (NCBI) 3, 132
RSP_1016 RSP_1016 small heat shock protein (NCBI) 3, 132
RSP_1058 RSP_1058 hypothetical transmemebrane protein (NCBI) 134, 216
RSP_1076 sohB Peptidase family S49 (NCBI) 216, 366
RSP_1077 RSP_1077 transcriptional regulator, LysR family (NCBI) 216, 249
RSP_1078 fdsG NAD-dependent formate dehydrogenase, gamma subunit (24 kDa) (NCBI) 216, 239
RSP_1079 fdsB NAD dependent formate dehydrogenase, beta subunit (51 kDa) (NCBI) 216, 239
RSP_1080 fdsA NAD-dependent formate dehydrogenase, alpha subunit (NCBI) 216, 239
RSP_1081 fdsC formate dehydrogenase chain C (NCBI) 216, 239
RSP_1082 fdsD NAD-dependent formate dehydrogenase, delta subunit (NCBI) 216, 239
RSP_1159 galU UDP-glucose pyrophosphate (NCBI) 132, 368
RSP_1173 dnaK Heat shock protein (Hsp70, DnaK (NCBI) 132, 297
RSP_1204 RSP_1204 ABC multidrug efflux pump, fused ATPase and inner membrane subunits (NCBI) 216, 237
RSP_1207 hslO putative Hsp33 protein (NCBI) 132, 366
RSP_1220 hrcA heat-inducible transcription repressor HrcA (NCBI) 10, 216
RSP_1270 RSP_1270 hypothetical protein (NCBI) 3, 132
RSP_1271 RSP_1271 periplasmic sensor signal transduction histidine kinase (NCBI) 3, 132
RSP_1272 RSP_1272 sigma24 (NCBI) 3, 132
RSP_1273 RSP_1273 hypothetical protein (NCBI) 3, 132
RSP_1274 RSP_1274 response regulator receiver protein (NCBI) 3, 132
RSP_1408 clpB Chaperone ClpB (NCBI) 132, 216
RSP_1531 RSP_1531 heat shock protein hslV, proteasome-related peptidase subunit (NCBI) 3, 132
RSP_1532 RSP_1532 Heat shock protein HslVU, ATPase subunit (NCBI) 132, 366
RSP_1563 RSP_1563 putative oxidoreductase (NCBI) 132, 366
RSP_1572 RSP_1572 Heat shock protein, Hsp20 family (NCBI) 3, 132
RSP_1573 RSP_1573 hypothetical protein (NCBI) 3, 132
RSP_1743 RSP_1743 ATPase, AAA family (NCBI) 216, 237
RSP_1873 RSP_1873 hypothetical protein (NCBI) 35, 216
RSP_2121 RSP_2121 hypothetical protein (NCBI) 216, 366
RSP_2130 RSP_2130 two component, sigma54 specific transcriptional regulator, fis family (NCBI) 132, 366
RSP_2196 RSP_2196 enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxybutyryl-CoA epimerase (NCBI) 174, 216
RSP_2197 RSP_2197 Acetoacetyl-CoA thiolase (NCBI) 174, 216
RSP_2638 RSP_2638 putative sodium/calcium exchanger (NCBI) 134, 216
RSP_2640 RSP_2640 hypothetical protein (NCBI) 134, 216
RSP_2657 xthA Exodeoxyribonuclease III (NCBI) 3, 132
RSP_2805 nemA Putative NADH-flavin oxidoreductase (NCBI) 3, 132
RSP_2864 cbbE Pentose-5-phosphate-3-epimerase (NCBI) 132, 264
RSP_2865 RSP_2865 putative transposase (NCBI) 132, 280
RSP_2966 uvrA ABC excinuclease subunit A (NCBI) 134, 216
RSP_3377 RSP_3377 Glutathione S-transferase family protein (NCBI) 176, 216
RSP_3602 RSP_3602 ABC efflux transporter, ATPase subunit (NCBI) 134, 216
RSP_3603 RSP_3603 Possible ABC efflux tranporter, fused inner membrane domains (NCBI) 134, 216
RSP_3686 RSP_3686 transcriptional regulator, LacI family (NCBI) 171, 216
RSP_3937 RSP_3937 probable transposase protein, Y4bF (NCBI) 11, 132
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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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.

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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.

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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.

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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.
  • 2. Source gene
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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