Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1077

transcriptional regulator, LysR family (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1077
(Mouseover regulator name to see its description)

RSP_1077 is regulated by 20 influences and regulates 26 modules.
Regulators for RSP_1077 (20)
Regulator Module Operator
RSP_1077 249 tf
RSP_1092 249 tf
RSP_1231 249 tf
RSP_2362 249 tf
RSP_2494 249 tf
RSP_3464 249 tf
RSP_3684 249 tf
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

Warning: RSP_1077 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
8152 1.10e+00 aTcGA.aAG.T
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8153 3.90e+03 AtGATCaCGat
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8216 3.40e+01 CttcGgGcCaaaggTCaCAAAaC
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8217 6.80e+02 ATCTtGT
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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_1077

RSP_1077 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for RSP_1077

RSP_1077 has total of 52 gene neighbors in modules 216, 249
Gene neighbors (52)
Gene Common Name Description Module membership
RSP_0328 nnrS hypothetical protein (NCBI) 168, 249
RSP_0351 RSP_0351 D-threo-aldose 1-dehydrogenase (NCBI) 158, 216
RSP_0360 RSP_0360 hypothetical protein (NCBI) 150, 249
RSP_0408 RSP_0408 hypothetical protein (NCBI) 134, 216
RSP_0410 RSP_0410 sensor diguanylate cyclase (GGDEF) (NCBI) 249, 282
RSP_0424 RSP_0424 hypothetical protein (NCBI) 216, 285
RSP_0470 RSP_0470 hypothetical protein (NCBI) 168, 249
RSP_0559 msrA Peptide methionine sulfoxide reductase (NCBI) 134, 216
RSP_0604 RSP_0604 hypothetical protein (NCBI) 29, 249
RSP_0605 RSP_0605 hypothetical protein (NCBI) 249, 370
RSP_0608 RSP_0608 hypothetical protein (NCBI) 146, 216
RSP_0614 RSP_0614 hypothetical protein (NCBI) 249, 325
RSP_0716 RSP_0716 NADPH/quinone reductase and related Zn-dependent oxidoreductases (NCBI) 132, 216
RSP_0952 RSP_0952 Transglutaminase-like protein (NCBI) 249, 370
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_1204 RSP_1204 ABC multidrug efflux pump, fused ATPase and inner membrane subunits (NCBI) 216, 237
RSP_1220 hrcA heat-inducible transcription repressor HrcA (NCBI) 10, 216
RSP_1408 clpB Chaperone ClpB (NCBI) 132, 216
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_2150 RSP_2150 predicted Glycosyl transferase, family 2 (NCBI) 138, 249
RSP_2151 yohD putative DedA family, membrane protein (NCBI) 138, 249
RSP_2152 RSP_2152 putative ceramide glucosyltransferase (NCBI) 138, 249
RSP_2153 RSP_2153 hypothetical protein (NCBI) 238, 249
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_2392 RSP_2392 putative membrane protein, similar to periplasmic nitrate reductase NnuR (NCBI) 249, 303
RSP_2638 RSP_2638 putative sodium/calcium exchanger (NCBI) 134, 216
RSP_2640 RSP_2640 hypothetical protein (NCBI) 134, 216
RSP_2700 RSP_2700 ABC oligo/dipeptide transporter, fused ATPase subunits (NCBI) 19, 249
RSP_2701 RSP_2701 ABC oligo/dipeptide transporter, inner membrane subunit (NCBI) 19, 249
RSP_2966 uvrA ABC excinuclease subunit A (NCBI) 134, 216
RSP_3043 RSP_3043 hypothetical protein (NCBI) 238, 249
RSP_3122 RSP_3122 putative Glutathione S-transferase (NCBI) 233, 249
RSP_3129 RSP_3129 serine/threonine protein kinase (NCBI) 244, 249
RSP_3131 RSP_3131 ABC (antimicrobial peptide) transporter, ATPase subunit (NCBI) 244, 249
RSP_3132 RSP_3132 hypothetical protein (NCBI) 244, 249
RSP_3133 RSP_3133 hypothetical protein (NCBI) 244, 249
RSP_3134 RSP_3134 Serine/threonine protein kinase (NCBI) 244, 249
RSP_3377 RSP_3377 Glutathione S-transferase family protein (NCBI) 176, 216
RSP_3576 RSP_3576 hypothetical protein (NCBI) 103, 249
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
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_1077
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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