Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0480 uxuB

D-mannonate oxidoreductase (NCBI)

CircVis
Functional Annotations (7)
Function System
Mannitol-1-phosphate/altronate dehydrogenases cog/ cog
metabolic process go/ biological_process
fructuronate reductase activity go/ molecular_function
oxidoreductase activity go/ molecular_function
coenzyme binding go/ molecular_function
Pentose and glucuronate interconversions kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0480
(Mouseover regulator name to see its description)

RSP_0480 is regulated by 18 influences and regulates 0 modules.
Regulators for RSP_0480 uxuB (18)
Regulator Module Operator
RSP_0386 337 tf
RSP_0489 337 tf
RSP_0507 337 tf
RSP_0547 337 tf
RSP_0999 337 tf
RSP_1871 337 tf
RSP_1890 337 tf
RSP_2719 337 tf
RSP_2800 337 tf
RSP_3094 337 tf
RSP_3165 337 tf
RSP_0443 301 tf
RSP_0489 301 tf
RSP_1092 301 tf
RSP_2324 301 tf
RSP_2572 301 tf
RSP_2719 301 tf
RSP_2850 301 tf

Warning: RSP_0480 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
8316 1.50e-04 tgaaGCATACTaGCATATTAGTca
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8317 1.70e+00 TTatcaGaGtCAttC
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8376 2.90e-10 ATTCaAAAAaAaatacaAAACaGA
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8377 1.50e-10 AtacCAagcGgTtTCAttTcctGA
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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_0480

RSP_0480 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Mannitol-1-phosphate/altronate dehydrogenases cog/ cog
metabolic process go/ biological_process
fructuronate reductase activity go/ molecular_function
oxidoreductase activity go/ molecular_function
coenzyme binding go/ molecular_function
Pentose and glucuronate interconversions kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for RSP_0480

RSP_0480 has total of 45 gene neighbors in modules 301, 337
Gene neighbors (45)
Gene Common Name Description Module membership
RSP_0480 uxuB D-mannonate oxidoreductase (NCBI) 301, 337
RSP_0481 RSP_0481 possible 2-deoxy-D-gluconate 3-dehydrogenase (NCBI) 253, 301
RSP_0482 kduI 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase (NCBI) 24, 301
RSP_0483 RSP_0483 hypothetical protein (NCBI) 295, 301
RSP_0484 RSP_0484 TRAP-T family transporter, DctM (12 TMs) subunit (NCBI) 295, 301
RSP_0485 RSP_0485 TRAP-T family transporter, DctQ (4 TMs) subunit (NCBI) 295, 301
RSP_0487 RSP_0487 TRAP-T family transporter, DctP (periplasmic binding) subunit (NCBI) 295, 301
RSP_0488 uxaC putative glucuronate isomerase (NCBI) 295, 301
RSP_0489 RSP_0489 GntR family transcriptional regulator (NCBI) 295, 301
RSP_0494 hypF hydrogenase maturation factor F (NCBI) 292, 337
RSP_0567 RSP_0567 Probable Methylated-DNA-(protein)-cysteine S-methyltransferase (NCBI) 316, 337
RSP_0773 RSP_0773 mannonate dehydratase (NCBI) 24, 301
RSP_0904 sitA ABC Mn+2/Fe+2 transporter, periplasmic substrate-binding protein SitA (NCBI) 266, 301
RSP_0905 sitB ABC Mn+2/Fe+2 transporter, ATPase subunit SitB (NCBI) 266, 301
RSP_0906 sitC ABC Mn+2/Fe+2 transporter, inner membrane subunit SitC (NCBI) 266, 301
RSP_0908 sitD ABC Mn+2/Fe+2 transporter, inner membrane subunit SitD (NCBI) 266, 301
RSP_1291 RSP_1291 ABC branched chain amino acid family transporter, periplasmic substrate binding protein (NCBI) 263, 337
RSP_1766 pykA Pyruvate kinase (NCBI) 203, 301
RSP_1839 RSP_1839 putative acetyltransferase, GNAT family (NCBI) 240, 337
RSP_2645 eda KDPG/KHG bifunctional aldolase (NCBI) 231, 301
RSP_2734 zwf Glucose-6-phosphate dehydrogenase (NCBI) 24, 301
RSP_2735 pgl 6-phosphogluconolactonase (NCBI) 24, 301
RSP_2736 pgi Phosphoglucose isomerase (PGI) glucose-6-phosphate isomerase (NCBI) 24, 301
RSP_2740 RSP_2740 putative Glucose/sorbosone dehydrogenase (NCBI) 148, 337
RSP_2779 catA Catalase (NCBI) 55, 301
RSP_2800 acoR Putative AcoR, Transcriptional activator of acetoin/glycerol metabolism (NCBI) 234, 337
RSP_3128 RSP_3128 hypothetical protein (NCBI) 292, 337
RSP_3165 RSP_3165 transcriptional regulator, GntR family (NCBI) 199, 337
RSP_3166 RSP_3166 ABC transporter, inner membrane subunit (NCBI) 199, 337
RSP_3167 RSP_3167 ABC transporter, ATPase subunit (NCBI) 199, 337
RSP_3168 RSP_3168 ABC transporter, periplasmic binding protein (NCBI) 199, 337
RSP_3169 RSP_3169 FAA-hydrolase-family protein (NCBI) 199, 337
RSP_3170 RSP_3170 Demethylmenaquinone methyltransferase (NCBI) 337, 356
RSP_3171 RSP_3171 3-hydroxyisobutyrate dehydrogenase (NCBI) 337, 356
RSP_3172 RSP_3172 hypothetical protein (NCBI) 337, 356
RSP_3223 RSP_3223 None 24, 337
RSP_3237 lguL Lactoylglutathione lyase (NCBI) 7, 301
RSP_3318 acrB Cation/multidrug efflux pump, RND family (NCBI) 301, 316
RSP_3321 acrA Cation/multidrug efflux pump, membrane-fusion protein (NCBI) 301, 316
RSP_3407 serA D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding subunit (NCBI) 61, 337
RSP_3408 dapA Dihydrodipicolinate synthetase (NCBI) 61, 337
RSP_3409 RSP_3409 TRAP-T family transporter, large (12 TMs) inner membrane subunit (NCBI) 61, 337
RSP_3410 RSP_3410 TRAP-T family transporter, periplasmic binding protein (NCBI) 61, 337
RSP_3411 RSP_3411 TRAP-T family transporter, small (4 TMs) inner membrane subunit (NCBI) 61, 337
RSP_3412 RSP_3412 Iron-containing alcohol dehydrogenase (NCBI) 61, 337
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_0480
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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