Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2300 atpC

ATP synthase, delta/epsilon subunit (NCBI)

CircVis
Functional Annotations (9)
Function System
F0F1-type ATP synthase, epsilon subunit (mitochondrial delta subunit) cog/ cog
hydrogen-transporting two-sector ATPase activity go/ molecular_function
ATP synthesis coupled proton transport go/ biological_process
proton-transporting ATP synthase complex go/ cellular_component
hydrogen ion transporting ATP synthase activity, rotational mechanism go/ molecular_function
proton-transporting ATPase activity, rotational mechanism go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
ATP_synt_epsi tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2300
(Mouseover regulator name to see its description)

RSP_2300 is regulated by 19 influences and regulates 0 modules.
Regulators for RSP_2300 atpC (19)
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_0327 15 tf
RSP_0755 15 tf
RSP_1231 15 tf
RSP_1739 15 tf
RSP_2236 15 tf
RSP_2533 15 tf
RSP_2681 15 tf
RSP_2838 15 tf
RSP_2840 15 tf
RSP_2922 15 tf
RSP_2950 15 tf
RSP_3095 15 tf

Warning: RSP_2300 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
7750 2.50e-05 atCGggAcagAAGG
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7751 1.60e-02 tGAAGGCtCTcCtCGGaaGcaTG
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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_2300

RSP_2300 is enriched for 9 functions in 3 categories.
Module neighborhood information for RSP_2300

RSP_2300 has total of 40 gene neighbors in modules 15, 369
Gene neighbors (40)
Gene Common Name Description Module membership
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_0239 PntB Pyridine nucleotide transhydrogenase beta subunit (NCBI) 15, 203
RSP_0240 pntA Pyridine nucleotide transhydrogenase alpha subunit (NCBI) 15, 203
RSP_0479 RSP_0479 Elongation factor P (EF-P) (NCBI) 345, 369
RSP_0568 RSP_0568 Isoleucyl-tRNA synthetase, class Ia (NCBI) 15, 258
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_1593 RSP_1593 NAD dependent malic enzyme (NCBI) 15, 25
RSP_1594 cdd Cytidine deaminase (NCBI) 15, 207
RSP_1595 RSP_1595 Thymidine phosphorylase (NCBI) 15, 25
RSP_1596 deoB probable phosphopentomutase protein (NCBI) 15, 174
RSP_1597 add adenosine deaminase (NCBI) 15, 174
RSP_1598 RSP_1598 putative uracil phosphoribosyltransferase (NCBI) 15, 25
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_1995 gltX Glutamyl-tRNA synthetase (NCBI) 15, 258
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
RSP_2894 ndk Nucleoside diphosphate kinase (NCBI) 15, 345
RSP_2895 RSP_2895 putative ABC transporter, fused ATPase subunits (NCBI) 15, 160
RSP_2896 RSP_2896 Multiple antibiotic transporter (NCBI) 15, 234
RSP_3074 ilvD Dihydroxy-acid and 6-phosphogluconate dehydratase (NCBI) 15, 309
RSP_4041 tyrS Tyrosyl-tRNA synthetase, class Ib (NCBI) 15, 258
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_2300
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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