Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2201

transcriptional regulator, MerR family (NCBI)

CircVis
Functional Annotations (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2201
(Mouseover regulator name to see its description)

RSP_2201 is regulated by 25 influences and regulates 7 modules.
Regulators for RSP_2201 (25)
Regulator Module Operator
RSP_0316 162 tf
RSP_0958 162 tf
RSP_0999 162 tf
RSP_1139 162 tf
RSP_1550 162 tf
RSP_1776 162 tf
RSP_1871 162 tf
RSP_2201 162 tf
RSP_2610 162 tf
RSP_3179 162 tf
RSP_3606 162 tf
RSP_0601 286 tf
RSP_0607 286 tf
RSP_0958 286 tf
RSP_1034 286 tf
RSP_1274 286 tf
RSP_1892 286 tf
RSP_1922 286 tf
RSP_2130 286 tf
RSP_2201 286 tf
RSP_2610 286 tf
RSP_3324 286 tf
RSP_3464 286 tf
RSP_3680 286 tf
RSP_3748 286 tf

Warning: RSP_2201 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
8044 1.80e-09 aaaCgAatGGcgGAAcGTcacgAa
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8045 6.20e+00 AAgGtGAtCgA
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8286 1.30e+00 cgaaggTcaGgcAaagGatcg
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8287 4.00e+02 GtCgTTTcaaaCattTcGcGG
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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_2201

RSP_2201 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for RSP_2201

RSP_2201 has total of 46 gene neighbors in modules 162, 286
Gene neighbors (46)
Gene Common Name Description Module membership
RSP_0024 rfbC Putative dTDP-4-dehydrorhamnose 3,5-epimerase (dTDP-L-rhamnose synthetase) (NCBI) 162, 207
RSP_0243 RSP_0243 putative lipoprotein (NCBI) 162, 262
RSP_0335 RSP_0335 Probable dicyclicGMP cyclasephosphodiesterase (NCBI) 52, 162
RSP_0339 RSP_0339 hypothetical protein (NCBI) 280, 286
RSP_0671 RSP_0671 ExbD/TolR family protein (NCBI) 286, 294
RSP_0672 TolQ Biopolymer transport protein, TolQ (NCBI) 277, 286
RSP_0761 RSP_0761 hypothetical protein (NCBI) 2, 162
RSP_0762 RSP_0762 transcriptional regulator, XRE family (NCBI) 127, 162
RSP_0763 aatA aspartate aminotransferase A (NCBI) 162, 240
RSP_0799 RSP_0799 hypothetical protein (NCBI) 286, 287
RSP_0868 RSP_0868 putative transcriptional regulator (NCBI) 162, 181
RSP_0871 patB putative aminotransferase (NCBI) 162, 207
RSP_0923 map1 Methionine aminopeptidase, subfamily 1 (NCBI) 84, 286
RSP_0924 cinA Predicted nucleotide-utilizing enzyme/competence-damage associated protein (NCBI) 71, 286
RSP_0925 yobR Putative acetyl transferase (NCBI) 84, 286
RSP_0926 RSP_0926 OmpA/MotB family protein (NCBI) 84, 286
RSP_0958 RSP_0958 RAM domain protein (NCBI) 82, 286
RSP_0999 RSP_0999 hypothetical protein (NCBI) 127, 162
RSP_1070 RSP_1070 hypothetical protein (NCBI) 81, 162
RSP_1260 RSP_1260 hypothetical protein (NCBI) 207, 286
RSP_1261 blrB blue-light receptor of the BLUF-family (NCBI) 81, 162
RSP_1399 RSP_1399 hypothetical protein (NCBI) 162, 262
RSP_1421 RSP_1421 hypothetical protein (NCBI) 286, 366
RSP_1522 RSP_1522 hypothetical protein (NCBI) 162, 341
RSP_1542 RSP_1542 ABC transporter, ATPase subunit (NCBI) 210, 286
RSP_1672 pdxJ PNP synthase, pyridoxal phosphate biosynthetic protein PdxJ (NCBI) 181, 286
RSP_1823 mog Molybdenum cofactor biosynthesis protein (NCBI) 35, 162
RSP_1870 RSP_1870 predicted hydrolase (NCBI) 63, 162
RSP_1871 RSP_1871 Transcriptional regulator, GntR family (NCBI) 162, 341
RSP_1956 RSP_1956 hypothetical protein (NCBI) 280, 286
RSP_2139 RSP_2139 hypothetical protein (NCBI) 127, 162
RSP_2201 RSP_2201 transcriptional regulator, MerR family (NCBI) 162, 286
RSP_2202 RSP_2202 hypothetical protein (NCBI) 52, 162
RSP_2330 leuA 2-Isopropylmalate synthase (NCBI) 185, 286
RSP_2374 RSP_2374 hypothetical protein (NCBI) 218, 286
RSP_2387 RSP_2387 hypothetical protein (NCBI) 71, 286
RSP_2400 RSP_2400 ABC putrescine transporter, ATPase subunit (NCBI) 127, 162
RSP_2419 RSP_2419 hypothetical protein (NCBI) 162, 223
RSP_2421 RSP_2421 hypothetical protein (NCBI) 35, 162
RSP_2646 RSP_2646 None 286, 309
RSP_2954 RSP_2954 hypothetical protein (NCBI) 81, 162
RSP_2955 RSP_2955 hypothetical protein (NCBI) 81, 162
RSP_2973 RSP_2973 Peroxiredoxin (NCBI) 158, 286
RSP_3324 RSP_3324 transcriptional regulator, LuxR family (NCBI) 46, 286
RSP_3606 RSP_3606 Sigma54-2 (RNA polymerase sigma-54 factor) (NCBI) 10, 162
RSP_4043 RSP_4043 Peptidylprolyl isomerase (NCBI) 162, 166
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_2201
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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