Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1739 rpoA

RNA polymerase, alpha chain (NCBI)

CircVis
Functional Annotations (13)
Function System
DNA-directed RNA polymerase, alpha subunit/40 kD subunit cog/ cog
DNA binding go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription, DNA-dependent go/ biological_process
protein dimerization activity go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
rpoA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1739
(Mouseover regulator name to see its description)

RSP_1739 is regulated by 13 influences and regulates 31 modules.
Regulators for RSP_1739 rpoA (13)
Regulator Module Operator
RSP_0794 369 tf
RSP_1231 369 tf
RSP_1704 369 tf
RSP_1739 369 tf
RSP_2346 369 tf
RSP_2533 369 tf
RSP_2950 369 tf
RSP_0395 151 tf
RSP_1163 151 tf
RSP_1669 151 tf
RSP_1704 151 tf
RSP_1739 151 tf
RSP_2591 151 tf

Warning: RSP_1739 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
8022 2.40e+01 taTtccAa.aCcTTTttT
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8023 9.00e+02 AaAagca.gAAA
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8434 1.10e+02 GCgAGGaA
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8435 3.10e+03 AagGGgA.aAa
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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_1739

RSP_1739 is enriched for 13 functions in 3 categories.
Enrichment Table (13)
Function System
DNA-directed RNA polymerase, alpha subunit/40 kD subunit cog/ cog
DNA binding go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription, DNA-dependent go/ biological_process
protein dimerization activity go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
rpoA tigr/ tigrfam
Module neighborhood information for RSP_1739

RSP_1739 has total of 35 gene neighbors in modules 151, 369
Gene neighbors (35)
Gene Common Name Description Module membership
RSP_0021 rpsI Probable ribosomal protein S9 (NCBI) 151, 224
RSP_0022 RSP_0022 Probable ribosomal protein L13 (NCBI) 151, 369
RSP_0097 smoM TRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM (NCBI) 291, 369
RSP_0142 RSP_0142 FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) (NCBI) 109, 369
RSP_0479 RSP_0479 Elongation factor P (EF-P) (NCBI) 345, 369
RSP_0655 RSP_0655 hypothetical protein (NCBI) 109, 369
RSP_0911 dctQ TRAP-T family C4-dicarboxylate transporter, DctQ (4TMs) subunit (NCBI) 363, 369
RSP_0912 dctM TRAP-T family C4-dicarboxylate transporter, DctM (12TMs) subunit (NCBI) 363, 369
RSP_1035 atpF FoF1 ATP synthase, subunit B (NCBI) 15, 369
RSP_1036 atpX FoF1 ATP synthase, subunit B (NCBI) 15, 369
RSP_1037 atpE FoF1 ATP synthase, subunit C (NCBI) 15, 369
RSP_1038 atpB FoF1 ATP synthase, subunit A (NCBI) 15, 369
RSP_1039 atpI FoF1 ATP synthase, subunit I (NCBI) 43, 369
RSP_1064 RSP_1064 Putative preprotein translocase, YidC (NCBI) 43, 369
RSP_1725 rplN Ribosomal protein L14 (NCBI) 151, 272
RSP_1726 rplX Ribosomal protein L24 (NCBI) 151, 272
RSP_1727 rplE Ribosomal protein L5 (NCBI) 151, 272
RSP_1728 rpsN Ribosomal protein S14 (NCBI) 151, 272
RSP_1729 rpsH Ribosomal protein S8 (NCBI) 151, 272
RSP_1730 rplF Ribosomal protein L6 (NCBI) 151, 272
RSP_1731 rplR Ribosomal protein L18 (NCBI) 151, 272
RSP_1737 rpsM Ribosomal protein S13 (NCBI) 151, 169
RSP_1738 rpsK Ribosomal protein S11 (NCBI) 151, 169
RSP_1739 rpoA RNA polymerase, alpha chain (NCBI) 151, 369
RSP_1740 rplQ Ribosomal protein L17 (NCBI) 151, 369
RSP_1798 SecD Protein-export membrane protein secD (NCBI) 224, 369
RSP_2221 purB Adenylosuccinate lyase (NCBI) 109, 369
RSP_2296 atpH ATPase, delta (OSCP) subunit (NCBI) 203, 369
RSP_2297 atpA F0F1-type ATP synthase alpha subunit (NCBI) 208, 369
RSP_2298 atpG ATP synthase, gamma subunit (NCBI) 15, 369
RSP_2299 atpD F1-ATP synthase beta subunit (NCBI) 15, 369
RSP_2300 atpC ATP synthase, delta/epsilon subunit (NCBI) 15, 369
RSP_2342 gpt Xanthine-Guanine phosphoribosyltransferase (NCBI) 361, 369
RSP_2460 alr alanine racemase (NCBI) 30, 369
RSP_2491 eno Enolase (NCBI) 224, 369
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_1739
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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