Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0297

ABC branched chain amino acid transporter, ATPase subunit (NCBI)

CircVis
Functional Annotations (5)
Function System
ABC-type branched-chain amino acid transport systems, ATPase component cog/ cog
ATP binding go/ molecular_function
ATPase activity go/ molecular_function
ABC transporters kegg/ kegg pathway
urea_trans_UrtE tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0297
(Mouseover regulator name to see its description)

RSP_0297 is regulated by 24 influences and regulates 0 modules.
Regulators for RSP_0297 (24)
Regulator Module Operator
RSP_0511 304 tf
RSP_1607 304 tf
RSP_1660 304 tf
RSP_2922 304 tf
RSP_2932 304 tf
RSP_3001 304 tf
RSP_3055 304 tf
RSP_3418 304 tf
RSP_3464 304 tf
RSP_3616 304 tf
RSP_3676 304 tf
RSP_3684 304 tf
RSP_0607 103 tf
RSP_1225 103 tf
RSP_1231 103 tf
RSP_1607 103 tf
RSP_1776 103 tf
RSP_2026 103 tf
RSP_2171 103 tf
RSP_2494 103 tf
RSP_2867 103 tf
RSP_2922 103 tf
RSP_3179 103 tf
RSP_3616 103 tf

Warning: RSP_0297 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
7926 6.50e-02 CcAGgatGAAag
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7927 1.50e+04 AAATAT
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8322 4.80e+04 AAACCTTA
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8323 6.20e+04 ACATGAAGA
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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_0297

RSP_0297 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
ABC-type branched-chain amino acid transport systems, ATPase component cog/ cog
ATP binding go/ molecular_function
ATPase activity go/ molecular_function
ABC transporters kegg/ kegg pathway
urea_trans_UrtE tigr/ tigrfam
Module neighborhood information for RSP_0297

RSP_0297 has total of 66 gene neighbors in modules 103, 304
Gene neighbors (66)
Gene Common Name Description Module membership
RSP_0134 RSP_0134 hypothetical protein (NCBI) 103, 183
RSP_0209 RSP_0209 possible prophage Lp3 protein 18 (NCBI) 103, 138
RSP_0297 RSP_0297 ABC branched chain amino acid transporter, ATPase subunit (NCBI) 103, 304
RSP_0298 RSP_0298 ABC branched chain amino acid transporter, ATPase subunit (NCBI) 103, 313
RSP_0299 RSP_0299 ABC branched chain amino acid transporter, inner membrane subunit (NCBI) 103, 313
RSP_0300 RSP_0300 ABC branched chain amino acid transporter, inner membrane subunit (NCBI) 103, 147
RSP_0477 RSP_0477 hypothetical protein (NCBI) 97, 103
RSP_0512 RSP_0512 multisensor hybrid histidine kinase (NCBI) 94, 304
RSP_0607 RSP_0607 sigma 24 (NCBI) 77, 103
RSP_0609 RSP_0609 hypothetical protein (NCBI) 146, 304
RSP_0617 RSP_0617 hypothetical protein (NCBI) 103, 325
RSP_0856 btaA S-adenosylmethionine-diacylglycerol 3-amino-3-carboxypropyl transferase (NCBI) 6, 304
RSP_0938 RSP_0938 hypothetical protein (NCBI) 304, 313
RSP_1294 RSP_1294 possible 2-oxoisovalerate dehydrogenase; E1 component, alpha and beta subunit (NCBI) 103, 217
RSP_1323 RSP_1323 hypothetical protein (NCBI) 116, 304
RSP_1500 RSP_1500 possible anti-sigma regulatory kinase (NCBI) 29, 304
RSP_1618 RSP_1618 hypothetical protein (NCBI) 62, 304
RSP_1651 RSP_1651 hypothetical protein (NCBI) 304, 313
RSP_1694 RSP_1694 Probable short-chain dehydrogenase/reductase (NCBI) 233, 304
RSP_1753 RSP_1753 hypothetical protein (NCBI) 304, 355
RSP_1933 RSP_1933 Outer membrane protein, OmpA/MotB family (NCBI) 103, 280
RSP_1954 RSP_1954 hypothetical protein (NCBI) 155, 304
RSP_2019 RSP_2019 hypothetical protein (NCBI) 103, 120
RSP_2022 RSP_2022 Cytochrome b/diheme cytochrome c hybrid protein (NCBI) 103, 229
RSP_2023 RSP_2023 hypothetical protein (NCBI) 229, 304
RSP_2026 RSP_2026 transcriptional regulator, AraC family (NCBI) 103, 176
RSP_2055 RSP_2055 hypothetical protein (NCBI) 103, 379
RSP_2068 RSP_2068 putative ClpP-like protease (NCBI) 235, 304
RSP_2070 RSP_2070 Putative Phage-related terminase (NCBI) 77, 304
RSP_2071 RSP_2071 hypothetical protein (NCBI) 77, 304
RSP_2105 RSP_2105 hypothetical protein (NCBI) 103, 325
RSP_2259 RSP_2259 Transmembrane protein (NCBI) 288, 304
RSP_2385 RSP_2385 hypothetical protein (NCBI) 103, 124
RSP_2441 tlpS Putative transducer like protein (NCBI) 304, 320
RSP_2769 RSP_2769 probable 5,10-methylenetetrahydrofolate reductase (NCBI) 238, 304
RSP_2792 RSP_2792 putative monooxygenase alpha subunit (NCBI) 77, 103
RSP_2793 RSP_2793 Putative reductase component of monooxygenase (NCBI) 103, 313
RSP_2794 RSP_2794 Putative monooxygenase beta subunit (NCBI) 103, 193
RSP_2795 RSP_2795 Putative regulatory protein of multicomponent monooxygenase (NCBI) 103, 193
RSP_2796 RSP_2796 hypothetical protein (NCBI) 77, 103
RSP_2798 groEL3 Putative chaperonin groEL (NCBI) 77, 103
RSP_2813 mttB putative trimethylamine methyltransferase protein (NCBI) 73, 304
RSP_3014 RSP_3014 putative aldolase protein (NCBI) 137, 304
RSP_3018 RSP_3018 putative acyl-CoA dehydrogenase (NCBI) 304, 370
RSP_3096 RSP_3096 hypothetical protein (NCBI) 168, 304
RSP_3098 qoxB QoxB, Quinol oxidase subunit II (NCBI) 168, 304
RSP_3103 RSP_3103 hypothetical protein (NCBI) 19, 304
RSP_3104 fdh Putative Glutathione-dependent formaldehyde dehydrogenase (NCBI) 288, 304
RSP_3204 RSP_3204 putative Oxidoreductase (NCBI) 124, 304
RSP_3230 RSP_3230 hypothetical protein (NCBI) 103, 279
RSP_3283 RSP_3283 myo-inositol 2-dehydrogenase (NCBI) 116, 304
RSP_3334 RSP_3334 HyuE hydantoin racemase (NCBI) 44, 103
RSP_3357 gpU putative phage tail protein U (NCBI) 40, 304
RSP_3358 gpX Phage tail component protein X (NCBI) 282, 304
RSP_3360 RSP_3360 Adenine specific DNA methyltransferase, D12 class (NCBI) 103, 342
RSP_3497 RSP_3497 Caspase-1, p20 (NCBI) 103, 168
RSP_3498 RSP_3498 Antifreeze protein, type I (NCBI) 103, 370
RSP_3541 RSP_3541 hypothetical protein (NCBI) 103, 242
RSP_3576 RSP_3576 hypothetical protein (NCBI) 103, 249
RSP_3577 gvpG putative gas vesicle synthesis protein (NCBI) 253, 304
RSP_3659 RSP_3659 Predicted amidohydrolase (NCBI) 288, 304
RSP_3682 RSP_3682 hypothetical protein (NCBI) 74, 304
RSP_3774 RSP_3774 hypothetical protein (NCBI) 304, 380
RSP_3775 RSP_3775 hypothetical protein (NCBI) 304, 380
RSP_3812 RSP_3812 recombinase (NCBI) 103, 189
RSP_3814 RSP_3814 hypothetical protein (NCBI) 189, 304
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_0297
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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