Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3072 sndh

putative L-sorbosone dehydrogenase (NCBI)

CircVis
Functional Annotations (8)
Function System
Glucose/sorbosone dehydrogenases cog/ cog
catalytic activity go/ molecular_function
Fructose and mannose metabolism kegg/ kegg pathway
Bisphenol degradation kegg/ kegg pathway
Chloroalkane and chloroalkene degradation kegg/ kegg pathway
Butanoate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3072
(Mouseover regulator name to see its description)

RSP_3072 is regulated by 18 influences and regulates 0 modules.
Regulators for RSP_3072 sndh (18)
Regulator Module Operator
RSP_0394 72 tf
RSP_1231 72 tf
RSP_1776 72 tf
RSP_2346 72 tf
RSP_2533 72 tf
RSP_2840 72 tf
RSP_2889 72 tf
RSP_2922 72 tf
RSP_3001 72 tf
RSP_3680 72 tf
RSP_0032 23 tf
RSP_0068 23 tf
RSP_0087 23 tf
RSP_0327 23 tf
RSP_1550 23 tf
RSP_2939 23 tf
RSP_3124 23 tf
RSP_3606 23 tf

Warning: RSP_3072 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
7766 2.30e+02 AtCcTTgTGAaa
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7767 9.40e-01 GCtTTCggcg
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7864 3.50e-07 AtagggCcg.ATCctcttgCcCTT
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7865 5.20e-05 AcTCaaGaAcAacACaAGccAAAC
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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_3072

RSP_3072 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Glucose/sorbosone dehydrogenases cog/ cog
catalytic activity go/ molecular_function
Fructose and mannose metabolism kegg/ kegg pathway
Bisphenol degradation kegg/ kegg pathway
Chloroalkane and chloroalkene degradation kegg/ kegg pathway
Butanoate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for RSP_3072

RSP_3072 has total of 48 gene neighbors in modules 23, 72
Gene neighbors (48)
Gene Common Name Description Module membership
RSP_0089 RSP_0089 hypothetical protein (NCBI) 23, 110
RSP_0180 RSP_0180 ABC nitrate/sulfonate/bicarbonate transporter, inner membrane subunit (NCBI) 23, 288
RSP_0657 RSP_0657 hypothetical protein (NCBI) 30, 72
RSP_0658 RSP_0658 Probable ATP-dependent helicase (NCBI) 30, 72
RSP_0659 RSP_0659 Putative metallo-phosphoesterase (NCBI) 30, 72
RSP_0678 RSP_0678 hypothetical protein (NCBI) 23, 329
RSP_0769 RSP_0769 Glutathione S-transferase (NCBI) 23, 71
RSP_0821 RSP_0821 Esterase/lipase/thioesterase (NCBI) 72, 356
RSP_0931 ialA NUDIX hydrolase (NCBI) 23, 240
RSP_0950 RSP_0950 Arginine utilization protein RocB (NCBI) 23, 133
RSP_1004 RSP_1004 hypothetical protein (NCBI) 23, 326
RSP_1086 sdh saccharopine dehydrogenase (NAD+, L-lysine forming) (NCBI) 72, 175
RSP_1160 kdsB CMP-2-keto-3-deoxyoctulaosonic acid synthetase (NCBI) 72, 184
RSP_1322 fhlB flagellar biosynthesis pathway, component FlhB (NCBI) 23, 242
RSP_1375 RSP_1375 hypothetical protein (NCBI) 72, 278
RSP_1415 RSP_1415 putative polysaccharide deacetylase (NCBI) 23, 329
RSP_1416 RSP_1416 hypothetical protein (NCBI) 23, 329
RSP_1417 RSP_1417 hypothetical protein (NCBI) 23, 133
RSP_1463 RSP_1463 Putative acyl-CoA transferase/carnitine dehydratase (NCBI) 23, 306
RSP_1523 RSP_1523 hypothetical protein (NCBI) 23, 174
RSP_1537 RSP_1537 hypothetical protein (NCBI) 23, 101
RSP_1754 RSP_1754 hypothetical protein (NCBI) 72, 384
RSP_1908 RSP_1908 outer membrane protein, OmpA/MotB family (NCBI) 72, 381
RSP_2017 RSP_2017 hypothetical protein (NCBI) 23, 126
RSP_2145 trgA Tellurite resistance protein (NCBI) 23, 121
RSP_2251 RSP_2251 putative beta-ketoadipate enol-lactone hydrolase (NCBI) 23, 220
RSP_2267 RSP_2267 hypothetical protein (NCBI) 39, 72
RSP_2286 RSP_2286 hypothetical protein (NCBI) 23, 35
RSP_2295 RSP_2295 hypothetical protein (NCBI) 23, 154
RSP_2332 RSP_2332 hypothetical protein (NCBI) 67, 72
RSP_2333 nadE NH3 dependent NAD synthetase, NadE (NCBI) 72, 299
RSP_2341 RSP_2341 putative aminotransferase protein / Aspartate aminotransferase (2.6.1.1) (NCBI) 72, 343
RSP_2343 RSP_2343 Putative threonine efflux protein, RhtB family (NCBI) 72, 343
RSP_2344 fabI1 enoyl-acyl carrier protein reductase (NCBI) 72, 200
RSP_2345 pdxH Pyridoxamine 5'-phosphate oxidase (NCBI) 72, 343
RSP_2354 RSP_2354 hypothetical protein (NCBI) 23, 83
RSP_2418 pldB putative Esterase/lipase/thioesterase (NCBI) 23, 357
RSP_2537 prfC Probable peptide chain release factor RF3 (NCBI) 72, 166
RSP_2544 RSP_2544 Protein-L-isoaspartate O-methyltransferase (NCBI) 7, 72
RSP_2545 surE Survival protein SurE (NCBI) 39, 72
RSP_2953 RSP_2953 glutaredoxin-related protein (NCBI) 23, 237
RSP_3072 sndh putative L-sorbosone dehydrogenase (NCBI) 23, 72
RSP_3101 RSP_3101 periplasmic sensor diguanylate cyclase/phosphodiesterase (NCBI) 23, 174
RSP_3211 cbiO ABC cobalt transporter, ATPase subunit, CbiO (NCBI) 23, 244
RSP_3511 RSP_3511 two component transcriptional regulator, winged helix family family (NCBI) 23, 239
RSP_3572 galM putative aldose 1-epimerase protein (NCBI) 23, 30
RSP_3771 RSP_3771 hypothetical protein (NCBI) 72, 213
RSP_3807 RSP_3807 hypothetical protein (NCBI) 23, 344
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_3072
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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