Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0704

ABC peptide transporter, substrate binding protein (NCBI)

CircVis
Functional Annotations (4)
Function System
ABC-type oligopeptide transport system, periplasmic component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0704
(Mouseover regulator name to see its description)

RSP_0704 is regulated by 23 influences and regulates 0 modules.
Regulators for RSP_0704 (23)
Regulator Module Operator
RSP_0032 63 tf
RSP_0443 63 tf
RSP_0489 63 tf
RSP_0774 63 tf
RSP_1231 63 tf
RSP_1243 63 tf
RSP_1925 63 tf
RSP_2610 63 tf
RSP_2889 63 tf
RSP_3309 63 tf
RSP_0032 239 tf
RSP_0443 239 tf
RSP_0601 239 tf
RSP_0611 239 tf
RSP_1040 239 tf
RSP_1077 239 tf
RSP_1890 239 tf
RSP_1990 239 tf
RSP_2200 239 tf
RSP_2800 239 tf
RSP_2853 239 tf
RSP_3418 239 tf
RSP_3686 239 tf

Warning: RSP_0704 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
7846 1.10e+00 ctt.ttGcagGtcgaGacGg
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7847 2.30e-02 aaaTttacccTgC.TCg.Aaa
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8196 5.70e-01 AggcaAcagCAAgatGAGAC
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8197 7.50e-01 Aa.ggtcaGGTCgAG.AcCtc
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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_0704

RSP_0704 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
ABC-type oligopeptide transport system, periplasmic component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
ABC transporters kegg/ kegg pathway
Module neighborhood information for RSP_0704

RSP_0704 has total of 37 gene neighbors in modules 63, 239
Gene neighbors (37)
Gene Common Name Description Module membership
RSP_0392 RSP_0392 probable lactoylglutathione lyase (NCBI) 107, 239
RSP_0398 RSP_0398 dehydrogenase (NCBI) 239, 278
RSP_0663 RSP_0663 Formate-tetrahydrofolate ligase (NCBI) 121, 239
RSP_0704 RSP_0704 ABC peptide transporter, substrate binding protein (NCBI) 63, 239
RSP_0935 RSP_0935 MiaB-like Radical SAM protein (NCBI) 63, 107
RSP_0936 dapF Diaminopimelate epimerase (NCBI) 63, 195
RSP_0960 RSP_0960 alcohol dehydrogenase (NCBI) 239, 325
RSP_1078 fdsG NAD-dependent formate dehydrogenase, gamma subunit (24 kDa) (NCBI) 216, 239
RSP_1079 fdsB NAD dependent formate dehydrogenase, beta subunit (51 kDa) (NCBI) 216, 239
RSP_1080 fdsA NAD-dependent formate dehydrogenase, alpha subunit (NCBI) 216, 239
RSP_1081 fdsC formate dehydrogenase chain C (NCBI) 216, 239
RSP_1082 fdsD NAD-dependent formate dehydrogenase, delta subunit (NCBI) 216, 239
RSP_1486 RSP_1486 regulatory protein, TetR family (NCBI) 239, 289
RSP_1767 RSP_1767 possible N-formylglutamate amidohydrolase (NCBI) 63, 184
RSP_1838 RSP_1838 hypothetical protein (NCBI) 63, 181
RSP_1869 RSP_1869 Putative oxidoreductase protein (NCBI) 63, 164
RSP_1870 RSP_1870 predicted hydrolase (NCBI) 63, 162
RSP_1878 lipB Lipoate-protein ligase B (NCBI) 63, 181
RSP_1896 RSP_1896 probable guanine deaminase (NCBI) 63, 126
RSP_1897 mgtE Mg/Co/Ni transporter, MgtE (NCBI) 63, 184
RSP_1898 RSP_1898 putative 5-formyltetrahydrofolate cyclo-ligase (NCBI) 63, 101
RSP_1925 RSP_1925 Transcriptional regulator, GntR family (NCBI) 63, 120
RSP_1980 glcB malate synthase G protein (NCBI) 148, 239
RSP_2294 gloB putative hydroxyacylglutathione hydrolase (glyoxalase II) (GLX II) protein (NCBI) 239, 280
RSP_2376 kbl 2-amino-3-ketobutyrate CoA ligase (NCBI) 97, 239
RSP_2816 RSP_2816 hypothetical protein (NCBI) 63, 178
RSP_2841 trkA potassium uptake tranporter, NAD-binding subunit, TrkA (NCBI) 63, 268
RSP_3161 RSP_3161 hypothetical protein (NCBI) 63, 174
RSP_3272 ggt Gamma-glutamyltranspeptidase (NCBI) 210, 239
RSP_3309 RSP_3309 transcriptional regulator, AraC family (NCBI) 63, 107
RSP_3509 expE1 Hemolysin-type calcium-binding region, RTX (NCBI) 33, 239
RSP_3510 RSP_3510 hypothetical protein (NCBI) 33, 239
RSP_3511 RSP_3511 two component transcriptional regulator, winged helix family family (NCBI) 23, 239
RSP_3512 RSP_3512 periplasmic sensor signal transduction histidine kinase (NCBI) 33, 239
RSP_3604 RSP_3604 Rhodanese-like protein (NCBI) 63, 195
RSP_3646 RSP_3646 DNA topology modulation kinase FlaR, putative (NCBI) 46, 63
RSP_3678 RSP_3678 Siderophore-interacting protein (NCBI) 24, 239
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_0704
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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