Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3125

transcriptional regulator, ArsR familyy (NCBI)

CircVis
Functional Annotations (4)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3125
(Mouseover regulator name to see its description)

RSP_3125 is regulated by 19 influences and regulates 4 modules.
Regulators for RSP_3125 (19)
Regulator Module Operator
RSP_0032 323 tf
RSP_1286 323 tf
RSP_1776 323 tf
RSP_1785 323 tf
RSP_1936 323 tf
RSP_2610 323 tf
RSP_2850 323 tf
RSP_3022 323 tf
RSP_3124 323 tf
RSP_3731 323 tf
RSP_0327 1 tf
RSP_0527 1 tf
RSP_1550 1 tf
RSP_1739 1 tf
RSP_1922 1 tf
RSP_1936 1 tf
RSP_3124 1 tf
RSP_3238 1 tf
RSP_3433 1 tf

Warning: RSP_3125 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
7724 2.40e+00 gCcgtt.CcgacGaccGcgagc.a
Loader icon
7725 1.00e+04 AAcaTG.aGATGT
Loader icon
8356 4.50e-08 aaaaAttttc.t.tGaTttTCa.t
Loader icon
8357 2.50e+01 aaagtaaacGaTaTtgATaaT
Loader icon
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_3125

RSP_3125 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for RSP_3125

RSP_3125 has total of 46 gene neighbors in modules 1, 323
Gene neighbors (46)
Gene Common Name Description Module membership
RSP_0008 RSP_0008 possible transporter, DME family, DMT superfamily (NCBI) 323, 340
RSP_0203 RSP_0203 signal transduction kinase protein (NCBI) 1, 329
RSP_0214 RSP_0214 possible uncharacterized phage protein (NCBI) 323, 325
RSP_0393 RSP_0393 probable riboflavin biosynthesis protein (NCBI) 107, 323
RSP_0416 RSP_0416 putative calcium-binding EF-hand domain protein (NCBI) 1, 273
RSP_0563 RSP_0563 putative site-specific recombinase (NCBI) 220, 323
RSP_0794 catR transcriptional regulator, LysR family (NCBI) 1, 338
RSP_0824 pth Peptidyl-tRNA hydrolase (NCBI) 142, 323
RSP_0825 ppnk probable inorganic polyphosphate/ATP-NAD kinase (NCBI) 1, 10
RSP_0953 RSP_0953 hypothetical protein (NCBI) 121, 323
RSP_1022 RSP_1022 conserved hypothetical protein (possibly transmembrane) (NCBI) 200, 323
RSP_1174 pip Prolyl aminopeptidase (NCBI) 35, 323
RSP_1365 RSP_1365 hypothetical protein (NCBI) 182, 323
RSP_1384 RSP_1384 hypothetical protein (NCBI) 10, 323
RSP_1474 nspC putative carboxynorspermidine decarboxylase protein (NCBI) 271, 323
RSP_1780 RSP_1780 hypothetical protein (NCBI) 285, 323
RSP_1894 RSP_1894 hypothetical protein (NCBI) 323, 381
RSP_1922 RSP_1922 Transcriptional regulator, GntR family, with aminotransferase domain (NCBI) 1, 176
RSP_1924 RSP_1924 BioY family protein (NCBI) 296, 323
RSP_1931 RSP_1931 Probable ATPase, AAA family (NCBI) 1, 220
RSP_1934 RSP_1934 Xanthine and CO dehydrogenases maturation factor XdhC/CoxF family (NCBI) 1, 338
RSP_1935 RSP_1935 Putative Xanthine and CO dehydrogenases maturation factor XdhC/CoxF family (NCBI) 1, 338
RSP_1936 RSP_1936 molybdopterin biosynthesis protein (NCBI) 1, 338
RSP_1993 RSP_1993 hypothetical protein (NCBI) 37, 323
RSP_2005 ybaU possible peptidyl-prolyl cis-trans isomerse (NCBI) 203, 323
RSP_2018 RSP_2018 hypothetical protein (NCBI) 308, 323
RSP_2215 RSP_2215 hypothetical protein (NCBI) 223, 323
RSP_2331 ppaZ PpaZ, a novel pseudoazurin precursor (Blue Copper Protein) (NCBI) 1, 302
RSP_2422 mgpS putative ATP-dependent helicase, MgpS (NCBI) 1, 261
RSP_2557 asnB putative asparagine synthetase (NCBI) 157, 323
RSP_2746 RSP_2746 hypothetical protein (NCBI) 323, 335
RSP_2825 cobK Putative precorrin-6x reductase (NCBI) 1, 10
RSP_2946 argC N-acetyl-gamma-glutamyl-phosphate reductase (NCBI) 299, 323
RSP_3022 RSP_3022 transcriptional regulator, TetR family (NCBI) 213, 323
RSP_3094 RSP_3094 Putative transmembrane anti-sigma factor (NCBI) 202, 323
RSP_3123 RSP_3123 hypothetical protein (NCBI) 1, 288
RSP_3124 RSP_3124 transcriptional regulator, LysR family (NCBI) 1, 323
RSP_3125 RSP_3125 transcriptional regulator, ArsR familyy (NCBI) 1, 323
RSP_3368 RSP_3368 periplasmic sensor diguanylate cyclase (NCBI) 1, 322
RSP_3422 RSP_3422 hypothetical protein (NCBI) 251, 323
RSP_3433 RSP_3433 transcriptionalregulator, CopG family (NCBI) 1, 238
RSP_3592 aroA EPSP synthase, 3-phosphoshikimate 1-carboxyvinyltransferase (NCBI) 203, 323
RSP_3675 RSP_3675 Esterase/lipase/thioesterase (NCBI) 44, 323
RSP_3677 RSP_3677 ABC sugar transporter, ATPase subunit (NCBI) 44, 323
RSP_3695 argE putative acetylornithine deacetylase (acetylornithinase) (NCBI) 1, 107
RSP_3832 cxp putative thermostable carboxypeptidase 1 (NCBI) 1, 52
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_3125
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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