Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2306

putative HAD superfamily protein (NCBI)

CircVis
Functional Annotations (4)
Function System
Predicted sugar phosphatases of the HAD superfamily cog/ cog
metabolic process go/ biological_process
hydrolase activity go/ molecular_function
HAD-SF-IIA-hyp4 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2306
(Mouseover regulator name to see its description)

RSP_2306 is regulated by 28 influences and regulates 0 modules.
Regulators for RSP_2306 (28)
Regulator Module Operator
RSP_0395 279 tf
RSP_0443 279 tf
RSP_0489 279 tf
RSP_0511 279 tf
RSP_0527 279 tf
RSP_1163 279 tf
RSP_1191 279 tf
RSP_1231 279 tf
RSP_1922 279 tf
RSP_2324 279 tf
RSP_2730 279 tf
RSP_2850 279 tf
RSP_3022 279 tf
RSP_3616 279 tf
RSP_0327 234 tf
RSP_0394 234 tf
RSP_0443 234 tf
RSP_0755 234 tf
RSP_1663 234 tf
RSP_1990 234 tf
RSP_2800 234 tf
RSP_2922 234 tf
RSP_3029 234 tf
RSP_3094 234 tf
RSP_3341 234 tf
RSP_3400 234 tf
RSP_3667 234 tf
RSP_3694 234 tf

Warning: RSP_2306 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
8186 3.20e-03 CCGcaACAGGAAgga
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8187 1.30e+03 ccaGtc.gttGAcAaaCcata
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8272 4.40e-07 CCTcTGcaaGgCGacttcTCaaG
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8273 1.90e+00 AaAcAGGA.CG
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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_2306

RSP_2306 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted sugar phosphatases of the HAD superfamily cog/ cog
metabolic process go/ biological_process
hydrolase activity go/ molecular_function
HAD-SF-IIA-hyp4 tigr/ tigrfam
Module neighborhood information for RSP_2306

RSP_2306 has total of 53 gene neighbors in modules 234, 279
Gene neighbors (53)
Gene Common Name Description Module membership
RSP_0163 RSP_0163 putative iron(III) ABC transporter, fused inner membrane subunits (NCBI) 115, 234
RSP_0358 gor probable glutathione reductase (NCBI) 234, 299
RSP_0364 RSP_0364 possible transporter, RarD family, DMT superfamily (NCBI) 38, 234
RSP_0418 RSP_0418 hypothetical protein (NCBI) 58, 234
RSP_0446 RSP_0446 Isocitrate dehydrogenase (NCBI) 279, 297
RSP_0551 RSP_0551 putative thymidylate kinase (NCBI) 234, 340
RSP_0561 RSP_0561 Transaldolase (NCBI) 279, 349
RSP_0562 RSP_0562 hypothetical protein (NCBI) 54, 279
RSP_0584 RSP_0584 Lysyl-tRNA synthetase (NCBI) 109, 279
RSP_0724 mscL Large-conductance mechanosensitive channel (NCBI) 59, 234
RSP_0729 lysA Orn/DAP/Arg decarboxylase, family 2 (NCBI) 54, 234
RSP_0755 nusB putative N utilization substance protein B (NCBI) 234, 240
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_0873 RSP_0873 N-formylmethionyl tRNA deformylase (NCBI) 279, 306
RSP_0883 RSP_0883 SmpB protein (NCBI) 277, 279
RSP_1045 trmD tRNA (guanine-N1-)-methyltransferase (NCBI) 279, 356
RSP_1233 maf putative Maf/YceF/YhdE family protein (NCBI) 87, 234
RSP_1306 RSP_1306 PAS sensor Signal Tranduction Histidine Kinase (NCBI) 4, 234
RSP_1350 serB phosphoserine phosphatase (NCBI) 258, 279
RSP_1389 aroC Chorismate synthase (NCBI) 181, 234
RSP_1391 thiB ABC thiamine transporter, periplasmic substrate-binding protein (NCBI) 121, 234
RSP_1392 thiP ABC thiamine transporter, inner membrane subunit (NCBI) 233, 234
RSP_1459 RSP_1459 hypothetical protein (NCBI) 93, 279
RSP_1461 kdtA Putative 3-deoxy-D-manno-octulosonic-acid transferase (NCBI) 184, 279
RSP_1462 lpxK Putative Tetraacyldisaccharide-1-P 4'-kinase (NCBI) 84, 234
RSP_1472 RSP_1472 hypothetical protein (NCBI) 113, 234
RSP_1800 RSP_1800 hypothetical protein (NCBI) 234, 293
RSP_1806 RSP_1806 aconitate hydratase (RefSeq) 279, 297
RSP_1928 dnaB Replicative DNA helicase, DnaB (NCBI) 76, 234
RSP_1994 gltA Citrate synthase (NCBI) 279, 309
RSP_2205 RSP_2205 hypothetical protein (NCBI) 67, 234
RSP_2206 RSP_2206 hypothetical protein (NCBI) 67, 234
RSP_2306 RSP_2306 putative HAD superfamily protein (NCBI) 234, 279
RSP_2407 RSP_2407 periplasmic sensor hybrid histidine kinase (NCBI) 234, 322
RSP_2492 RSP_2492 Possible transporter, RhaT family, DMT superfamily (NCBI) 54, 234
RSP_2800 acoR Putative AcoR, Transcriptional activator of acetoin/glycerol metabolism (NCBI) 234, 337
RSP_2817 aroK Putative shikimate kinase (NCBI) 26, 234
RSP_2818 aroB Putative 3-dehydroquinate synthase (NCBI) 84, 234
RSP_2845 RSP_2845 putative penicillin acylase (penicillin amidase) (NCBI) 195, 279
RSP_2896 RSP_2896 Multiple antibiotic transporter (NCBI) 15, 234
RSP_2910 RSP_2910 Predicted Metal-dependent amidase/aminoacylase/carboxypeptidase (NCBI) 98, 279
RSP_2912 RSP_2912 Predicted pyrophosphatase (NCBI) 279, 356
RSP_3230 RSP_3230 hypothetical protein (NCBI) 103, 279
RSP_3231 RSP_3231 ABC peptide transporter, periplasmic binding protein (NCBI) 195, 279
RSP_3232 RSP_3232 ABC peptide transporter, inner membrane subunit (NCBI) 279, 297
RSP_3233 RSP_3233 ABC peptide transporter, inner membrane subunit (NCBI) 279, 297
RSP_3235 RSP_3235 ABC peptide transporter, ATPase subunit (NCBI) 279, 297
RSP_3236 RSP_3236 ABC peptide transporter, ATPase subunit (NCBI) 279, 297
RSP_3328 RSP_3328 hypothetical protein (NCBI) 279, 306
RSP_3716 selD selenide, water dikinase (selenophosphate synthetase) (NCBI) 279, 311
RSP_3749 ampC putative beta-lactamase precursor (NCBI) 279, 362
RSP_3822 RSP_3822 GTP1/OBG family protein (NCBI) 30, 279
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_2306
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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