Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3606

Sigma54-2 (RNA polymerase sigma-54 factor) (NCBI)

CircVis
Functional Annotations (10)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
Two-component system kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
rpoN_sigma tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3606
(Mouseover regulator name to see its description)

RSP_3606 is regulated by 22 influences and regulates 16 modules.
Regulators for RSP_3606 (22)
Regulator Module Operator
RSP_0122 10 tf
RSP_0316 10 tf
RSP_0327 10 tf
RSP_0999 10 tf
RSP_1139 10 tf
RSP_1220 10 tf
RSP_1550 10 tf
RSP_1739 10 tf
RSP_1871 10 tf
RSP_3238 10 tf
RSP_3606 10 tf
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

Warning: RSP_3606 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
7740 3.00e-03 atgtttc.aTttcCTGcaaagCTg
Loader icon
7741 9.60e+01 AAtccgctGCaaAt.tta.cG
Loader icon
8044 1.80e-09 aaaCgAatGGcgGAAcGTcacgAa
Loader icon
8045 6.20e+00 AAgGtGAtCgA
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_3606

RSP_3606 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
Two-component system kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
rpoN_sigma tigr/ tigrfam
Module neighborhood information for RSP_3606

RSP_3606 has total of 53 gene neighbors in modules 10, 162
Gene neighbors (53)
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_0419 RSP_0419 hypothetical protein (NCBI) 10, 308
RSP_0674 RSP_0674 Putative HolB DNA polymerase III delta prime subunit (NCBI) 10, 36
RSP_0715 RSP_0715 Ribonuclease T2 (NCBI) 10, 35
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_0765 RSP_0765 SAM-dependent methyltransferase (NCBI) 10, 176
RSP_0766 RSP_0766 hypothetical protein (NCBI) 10, 56
RSP_0825 ppnk probable inorganic polyphosphate/ATP-NAD kinase (NCBI) 1, 10
RSP_0845 RSP_0845 hypothetical protein (NCBI) 4, 10
RSP_0846 ribA GTP cyclohydrolase II (NCBI) 4, 10
RSP_0847 RSP_0847 two component transcriptional regulator, winged helix family (NCBI) 10, 287
RSP_0868 RSP_0868 putative transcriptional regulator (NCBI) 162, 181
RSP_0871 patB putative aminotransferase (NCBI) 162, 207
RSP_0897 RSP_0897 Glutathione S-transferase (NCBI) 10, 20
RSP_0999 RSP_0999 hypothetical protein (NCBI) 127, 162
RSP_1006 RSP_1006 hypothetical protein (NCBI) 7, 10
RSP_1007 RSP_1007 hypothetical protein (NCBI) 10, 127
RSP_1070 RSP_1070 hypothetical protein (NCBI) 81, 162
RSP_1220 hrcA heat-inducible transcription repressor HrcA (NCBI) 10, 216
RSP_1261 blrB blue-light receptor of the BLUF-family (NCBI) 81, 162
RSP_1384 RSP_1384 hypothetical protein (NCBI) 10, 323
RSP_1399 RSP_1399 hypothetical protein (NCBI) 162, 262
RSP_1522 RSP_1522 hypothetical protein (NCBI) 162, 341
RSP_1794 RSP_1794 putative lytic transglycosylase (NCBI) 10, 250
RSP_1823 mog Molybdenum cofactor biosynthesis protein (NCBI) 35, 162
RSP_1834 RSP_1834 hypothetical protein (NCBI) 10, 185
RSP_1868 RSP_1868 serine-pyruvate aminotransferase (NCBI) 10, 127
RSP_1870 RSP_1870 predicted hydrolase (NCBI) 63, 162
RSP_1871 RSP_1871 Transcriptional regulator, GntR family (NCBI) 162, 341
RSP_1891 RSP_1891 Zinc-binding dehydrogenase (NCBI) 10, 158
RSP_2119 RSP_2119 hypothetical protein (NCBI) 10, 381
RSP_2120 RSP_2120 putative D-lactate dehydrogenase (cytochrome), FAD/FMN-containing oxidoreductase (NCBI) 10, 127
RSP_2139 RSP_2139 hypothetical protein (NCBI) 127, 162
RSP_2142 RSP_2142 NifS-related protein (NCBI) 4, 10
RSP_2201 RSP_2201 transcriptional regulator, MerR family (NCBI) 162, 286
RSP_2202 RSP_2202 hypothetical protein (NCBI) 52, 162
RSP_2282 chrA Chromate efflux pump, ChrA (NCBI) 10, 107
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_2505 creA possible CreA protein (NCBI) 10, 237
RSP_2551 exoO Glycosyl transferase, family 2 (NCBI) 10, 100
RSP_2618 RSP_2618 Putative hemolysin (NCBI) 10, 341
RSP_2825 cobK Putative precorrin-6x reductase (NCBI) 1, 10
RSP_2954 RSP_2954 hypothetical protein (NCBI) 81, 162
RSP_2955 RSP_2955 hypothetical protein (NCBI) 81, 162
RSP_3606 RSP_3606 Sigma54-2 (RNA polymerase sigma-54 factor) (NCBI) 10, 162
RSP_3836 RSP_3836 Putative metal-dependent hydrolase (NCBI) 10, 329
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_3606
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