Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3095

sigma24 (NCBI)

CircVis
Functional Annotations (7)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog cog/ cog
sequence-specific DNA binding transcription factor 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
RNA polymerase kegg/ kegg pathway
sigma70-ECF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3095
(Mouseover regulator name to see its description)

RSP_3095 is regulated by 20 influences and regulates 8 modules.
Regulators for RSP_3095 (20)
Regulator Module Operator
RSP_0601 202 tf
RSP_1040 202 tf
RSP_1776 202 tf
RSP_2130 202 tf
RSP_2425 202 tf
RSP_3094 202 tf
RSP_3095 202 tf
RSP_0511 168 tf
RSP_1014 168 tf
RSP_1231 168 tf
RSP_1867 168 tf
RSP_2165 168 tf
RSP_2494 168 tf
RSP_2533 168 tf
RSP_2867 168 tf
RSP_3203 168 tf
RSP_3464 168 tf
RSP_3684 168 tf
RSP_3731 168 tf
RSP_3748 168 tf

Warning: RSP_3095 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
8056 1.30e+03 AtATaCa.aG..TTt
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8057 4.50e+03 Cag.cgggccgGaTCGggCat
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8124 1.70e-01 CcataccAaCCccgAtatGgCGCG
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8125 1.60e+00 CAAG..g.tcGAgagAgaaGA
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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_3095

RSP_3095 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog cog/ cog
sequence-specific DNA binding transcription factor 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
RNA polymerase kegg/ kegg pathway
sigma70-ECF tigr/ tigrfam
Module neighborhood information for RSP_3095

RSP_3095 has total of 43 gene neighbors in modules 168, 202
Gene neighbors (43)
Gene Common Name Description Module membership
RSP_0088 RSP_0088 ycfI, putative structural proteins (NCBI) 73, 168
RSP_0219 RSP_0219 hypothetical protein (NCBI) 168, 220
RSP_0328 nnrS hypothetical protein (NCBI) 168, 249
RSP_0470 RSP_0470 hypothetical protein (NCBI) 168, 249
RSP_0511 RSP_0511 two component transcriptional regulator, LuxR family (NCBI) 168, 176
RSP_0524 RSP_0524 hypothetical protein (NCBI) 74, 168
RSP_0801 RSP_0801 deacetylase / probable acetylpolyamine aminohydrolase (NCBI) 168, 242
RSP_0864 RSP_0864 Puative heme-binding hypothetical protein (NCBI) 168, 238
RSP_0947 RSP_0947 hypothetical protein (NCBI) 168, 213
RSP_0951 RSP_0951 hypothetical protein (NCBI) 168, 238
RSP_1210 RSP_1210 Response regulator receiver protein (NCBI) 73, 168
RSP_1237 secB Preprotein translocase subunit SecB (NCBI) 202, 366
RSP_1238 fxsA putative FxsA cytoplasmic membrane protein (NCBI) 202, 366
RSP_1239 RSP_1239 hypothetical protein (NCBI) 202, 366
RSP_1240 RSP_1240 putative membrane-bound lytic murein transglycosylase A transmembrane protein (NCBI) 202, 366
RSP_1300 RSP_1300 hypothetical protein (NCBI) 168, 303
RSP_1640 RSP_1640 hypothetical protein (NCBI) 168, 233
RSP_2125 RSP_2125 hypothetical protein (NCBI) 202, 366
RSP_2627 hisI Phosphoribosyl-AMP cyclohydrolase (NCBI) 202, 277
RSP_2632 argI Arginase (NCBI) 95, 168
RSP_2791 RSP_2791 hypothetical protein (NCBI) 168, 236
RSP_2957 RSP_2957 hypothetical protein (NCBI) 168, 213
RSP_3026 RSP_3026 Transcriptional regulator, MocR family (NCBI) 83, 168
RSP_3037 RSP_3037 Putative short-chain dehydrogenase/reductase (NCBI) 57, 168
RSP_3050 moaA Molybdenum cofactor biosynthesis protein A (NCBI) 168, 308
RSP_3092 RSP_3092 hypothetical protein (NCBI) 202, 368
RSP_3093 RSP_3093 Predicted integral membrane protein (NCBI) 202, 368
RSP_3094 RSP_3094 Putative transmembrane anti-sigma factor (NCBI) 202, 323
RSP_3095 RSP_3095 sigma24 (NCBI) 168, 202
RSP_3096 RSP_3096 hypothetical protein (NCBI) 168, 304
RSP_3098 qoxB QoxB, Quinol oxidase subunit II (NCBI) 168, 304
RSP_3137 RSP_3137 hypothetical protein (NCBI) 141, 168
RSP_3213 RSP_3213 hypothetical protein (NCBI) 168, 313
RSP_3257 RSP_3257 ABC peptide transporter, inner membrane subunit (NCBI) 168, 325
RSP_3343 RSP_3343 putative glycosyl transferase (NCBI) 14, 168
RSP_3444 RSP_3444 Putative Xaa-Pro aminopeptidase (NCBI) 61, 168
RSP_3446 RSP_3446 Putative amino acid hydrolase (NCBI) 61, 168
RSP_3447 RSP_3447 Putative dehydrogenase (NCBI) 61, 168
RSP_3497 RSP_3497 Caspase-1, p20 (NCBI) 103, 168
RSP_3552 RSP_3552 hypothetical protein (NCBI) 202, 366
RSP_3566 RSP_3566 dimethylglycine dehydrogenase (NCBI) 27, 168
RSP_3601 RSP_3601 Lipolytic enzyme, G-D-S-L family (NCBI) 134, 202
RSP_3793 RSP_3793 hypothetical protein (NCBI) 73, 168
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_3095
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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