Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1206

putative phosphohydrolase (mutT/nudix family protein) (NCBI)

CircVis
Functional Annotations (2)
Function System
NTP pyrophosphohydrolases including oxidative damage repair enzymes cog/ cog
hydrolase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1206
(Mouseover regulator name to see its description)

RSP_1206 is regulated by 20 influences and regulates 0 modules.
Regulators for RSP_1206 (20)
Regulator Module Operator
RSP_0774 149 tf
RSP_1163 149 tf
RSP_1231 149 tf
RSP_1663 149 tf
RSP_1776 149 tf
RSP_1892 149 tf
RSP_2130 149 tf
RSP_2939 149 tf
RSP_3001 149 tf
RSP_0386 54 tf
RSP_0774 54 tf
RSP_1606 54 tf
RSP_1892 54 tf
RSP_2165 54 tf
RSP_2410 54 tf
RSP_2533 54 tf
RSP_2850 54 tf
RSP_2888 54 tf
RSP_3309 54 tf
RSP_3341 54 tf

Warning: RSP_1206 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
7828 3.40e+00 TAtcgCATcGGcGcGgatgGGaAA
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7829 2.40e+03 AAgaatTtcctggggAtcTTCCtT
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8018 1.90e+03 atATAGga
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8019 1.20e+04 GacCtt.A.CAAgGgaTT
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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_1206

RSP_1206 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
NTP pyrophosphohydrolases including oxidative damage repair enzymes cog/ cog
hydrolase activity go/ molecular_function
Module neighborhood information for RSP_1206

RSP_1206 has total of 40 gene neighbors in modules 54, 149
Gene neighbors (40)
Gene Common Name Description Module membership
RSP_0560 priA Probable pimosomal protein N' (NCBI) 54, 340
RSP_0562 RSP_0562 hypothetical protein (NCBI) 54, 279
RSP_0681 RSP_0681 hypothetical protein (NCBI) 54, 243
RSP_0729 lysA Orn/DAP/Arg decarboxylase, family 2 (NCBI) 54, 234
RSP_0730 RSP_0730 hypothetical protein (NCBI) 2, 54
RSP_0743 RSP_0743 Putative translation factor (NCBI) 149, 299
RSP_0830 RSP_0830 CBS-domain-containing membrane protein (NCBI) 54, 69
RSP_1014 RSP_1014 sigma24 (NCBI) 54, 236
RSP_1015 RSP_1015 Putative membrane protein with von Willebrand (VWA) domain (NCBI) 54, 124
RSP_1106 rbfA Ribosome-binding factor A (NCBI) 46, 149
RSP_1107 RSP_1107 hypothetical protein (NCBI) 134, 149
RSP_1130 RSP_1130 hypothetical membrane protein (NCBI) 54, 91
RSP_1158 PtsN PTS IIA-like nitrogen-regulatory protein PtsN (NCBI) 149, 181
RSP_1206 RSP_1206 putative phosphohydrolase (mutT/nudix family protein) (NCBI) 54, 149
RSP_1286 cbbR RuBisCO operon transcriptional regulator, CbbR (NCBI) 54, 340
RSP_1414 RSP_1414 hypothetical protein (NCBI) 54, 94
RSP_1510 RSP_1510 Putative glycerol-3-phosphate dehydrogenase (NAD(P)+) (NCBI) 149, 354
RSP_1564 RSP_1564 Putative transmembrane transport protein (NCBI) 149, 366
RSP_1576 trxB Thioredoxin reductase (NCBI) 149, 366
RSP_1635 RSP_1635 hypothetical protein (NCBI) 31, 54
RSP_1801 ccmA ABC heme exporter, ATPase subunt CcmA (NCBI) 149, 299
RSP_1803 ccmC ABC heme exporter, inner membrane subunit CcmC (NCBI) 149, 299
RSP_1804 ccmD Heme exporter protein D (NCBI) 149, 299
RSP_1805 ccmG Probable thiol-disulfide interchange protein (NCBI) 149, 299
RSP_2015 argK ATPase (NCBI) 54, 113
RSP_2075 RSP_2075 Putative Transcriptional regulator (NCBI) 54, 213
RSP_2163 RSP_2163 lytic murein transglycosylase, putative (NCBI) 149, 349
RSP_2245 hisH Glutamine amidotransferase (NCBI) 149, 181
RSP_2302 RSP_2302 putative low specificity L-threonine aldolase (NCBI) 54, 146
RSP_2303 RSP_2303 hypothetical protein (NCBI) 54, 271
RSP_2409 rluD putative Pseudouridine synthase, Rlu (NCBI) 54, 316
RSP_2492 RSP_2492 Possible transporter, RhaT family, DMT superfamily (NCBI) 54, 234
RSP_2850 mfd transcription-repair coupling factor (helicase) (NCBI) 54, 340
RSP_2971 RSP_2971 S-adenosylmethionine tRNA ribosyltransferase-isomerase (NCBI) 54, 218
RSP_2972 RSP_2972 hypothetical protein (NCBI) 54, 158
RSP_3091 RSP_3091 Coserved hypothetical protein (NCBI) 54, 84
RSP_3126 RSP_3126 Arsenite efflux pump, ACR3 family (NCBI) 54, 196
RSP_3127 arsC Putative arsenate reductase (NCBI) 54, 181
RSP_3426 RSP_3426 hypothetical protein (NCBI) 149, 365
RSP_3430 RSP_3430 transcriptional regulator, winged helix family (NCBI) 54, 121
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_1206
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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