Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3249

ABC peptide transporter, duplicated ATPase domains (NCBI)

CircVis
Functional Annotations (5)
Function System
ATPase components of various ABC-type transport systems, contain duplicated ATPase cog/ cog
ATP binding go/ molecular_function
peptide transport go/ biological_process
ATPase activity go/ molecular_function
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3249
(Mouseover regulator name to see its description)

RSP_3249 is regulated by 18 influences and regulates 0 modules.
Regulators for RSP_3249 (18)
Regulator Module Operator
RSP_0014 267 tf
RSP_0386 267 tf
RSP_0623 267 tf
RSP_1092 267 tf
RSP_1225 267 tf
RSP_1231 267 tf
RSP_2425 267 tf
RSP_2950 267 tf
RSP_3317 267 tf
RSP_0607 362 tf
RSP_0623 362 tf
RSP_1014 362 tf
RSP_1776 362 tf
RSP_2351 362 tf
RSP_2494 362 tf
RSP_2867 362 tf
RSP_2965 362 tf
RSP_3464 362 tf

Warning: RSP_3249 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
8252 4.40e+02 GGccTTgcacccgaT
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8253 2.10e+02 TTctgcGAaGCt.cccgA
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8422 1.20e-06 aAaggGcgggAccGCacagAagcg
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8423 3.10e-06 gGtgGGggCGGTCTAtccggGCc
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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_3249

RSP_3249 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
ATPase components of various ABC-type transport systems, contain duplicated ATPase cog/ cog
ATP binding go/ molecular_function
peptide transport go/ biological_process
ATPase activity go/ molecular_function
ABC transporters kegg/ kegg pathway
Module neighborhood information for RSP_3249

RSP_3249 has total of 46 gene neighbors in modules 267, 362
Gene neighbors (46)
Gene Common Name Description Module membership
RSP_0113 RSP_0113 Phospholipase D/Transphosphatidylase (NCBI) 176, 362
RSP_0318 RSP_0318 hypothetical protein (NCBI) 116, 362
RSP_0319 RSP_0319 NnrU (NCBI) 116, 362
RSP_0320 NnrT NnrT (NCBI) 116, 362
RSP_0321 norD NorD Nitric oxide reductase activation protein (NCBI) 116, 362
RSP_0322 norQ NorQ protein required for nitric oxide reductase activity (NCBI) 116, 362
RSP_0323 norB Nitric oxide reductase large subunit, cytochrome b (NCBI) 116, 362
RSP_0324 norC nitric oxide reductase subunit C, cytochrome c (NCBI) 116, 362
RSP_0325 RSP_0325 hypothetical protein (NCBI) 116, 362
RSP_0349 RSP_0349 ABC transporter, ATPase subunit (NCBI) 267, 293
RSP_0369 RSP_0369 hypothetical protein (NCBI) 47, 267
RSP_0459 RSP_0459 hypothetical protein (NCBI) 47, 267
RSP_0572 RSP_0572 putative exonuclease (NCBI) 22, 362
RSP_0573 phoB Response regulator receiver protein (NCBI) 22, 362
RSP_0574 RSP_0574 hypothetical protein (NCBI) 22, 362
RSP_0575 RSP_0575 Predicted signal transduction protein containing cyclic nucleotide-binding and CBS domains (NCBI) 22, 362
RSP_0772 parE DNA topoisomerase II/DNA gyrase, subunit B (NCBI) 69, 267
RSP_1013 RSP_1013 possible Hemolysin (NCBI) 68, 267
RSP_1069 RSP_1069 hypothetical protein (NCBI) 233, 267
RSP_1170 RSP_1170 OmpA family protein (NCBI) 267, 355
RSP_1235 coaE Dephospho-CoA kinase (NCBI) 87, 267
RSP_1236 dnaQ putative DNA polymerase III, epsilon subunit and related 3'-5' exonucleases (NCBI) 87, 267
RSP_1293 RSP_1293 putative acyl-carrier protein (NCBI) 267, 380
RSP_1348 RSP_1348 hypothetical protein (NCBI) 280, 362
RSP_1349 RSP_1349 hypothetical protein (NCBI) 160, 362
RSP_1503 RSP_1503 hypothetical protein (NCBI) 265, 267
RSP_1673 RSP_1673 Probable holo-acyl carrier protein synthase (NCBI) 265, 267
RSP_1683 RSP_1683 putative kinase/phosphatase (NCBI) 267, 341
RSP_2081 RSP_2081 putative acetyltransferase, GNAT family (NCBI) 87, 267
RSP_2212 rimI putative acetyltransferase (NCBI) 159, 267
RSP_2260 ydjG hypothetical protein (NCBI) 267, 342
RSP_2326 pbpA Cell division protein FtsI (NCBI) 47, 267
RSP_2351 RSP_2351 hypothetical protein (NCBI) 74, 362
RSP_2357 RSP_2357 hypothetical protein (NCBI) 288, 362
RSP_2457 RSP_2457 hypothetical protein (NCBI) 30, 267
RSP_2567 sqdC putative sulfolipid biosynthesis protein (NCBI) 47, 267
RSP_2628 gltX/glnS glutamyl-/ glutaminyl-tRNA synthetase (NCBI) 65, 267
RSP_2676 RSP_2676 hypothetical protein (NCBI) 73, 362
RSP_2905 ksgA Putative ribosomal RNA adenine dimethylase (NCBI) 87, 267
RSP_3249 RSP_3249 ABC peptide transporter, duplicated ATPase domains (NCBI) 267, 362
RSP_3250 RSP_3250 ABC peptide transporter, inner membrane subunit (NCBI) 267, 340
RSP_3251 RSP_3251 ABC peptide transporter, inner membrane subunit (NCBI) 267, 362
RSP_3301 eda 2-dehydro-3-deoxyphosphogluconate aldolase (NCBI) 265, 267
RSP_3373 RSP_3373 ABC efflux transporter, inner membrane subunit (NCBI) 42, 267
RSP_3748 ampR transcriptional regulator, LysR family (NCBI) 97, 362
RSP_3749 ampC putative beta-lactamase precursor (NCBI) 279, 362
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_3249
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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