Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2397

ABC putrescine transporter, periplasmic substrate-binding subunit (NCBI)

CircVis
Functional Annotations (4)
Function System
Spermidine/putrescine-binding periplasmic protein cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
outer membrane-bounded periplasmic space go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2397
(Mouseover regulator name to see its description)

RSP_2397 is regulated by 18 influences and regulates 0 modules.
Regulators for RSP_2397 (18)
Regulator Module Operator
RSP_0014 291 tf
RSP_0316 291 tf
RSP_0327 291 tf
RSP_0402 291 tf
RSP_1139 291 tf
RSP_1191 291 tf
RSP_1231 291 tf
RSP_2130 291 tf
RSP_2591 291 tf
RSP_2681 291 tf
RSP_2853 291 tf
RSP_3202 291 tf
RSP_0087 70 tf
RSP_0386 70 tf
RSP_1191 70 tf
RSP_1866 70 tf
RSP_2681 70 tf
RSP_3238 70 tf

Warning: RSP_2397 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
7860 2.20e-03 agAAttct.TT
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7861 3.70e-01 TTtTcatgttttc.g
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8296 9.20e-04 GCtTtGacgGcaccga.tTgTCgC
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8297 2.30e+02 aaGCCaCCCcaTGCGgcgtaa
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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_2397

RSP_2397 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Spermidine/putrescine-binding periplasmic protein cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
outer membrane-bounded periplasmic space go/ cellular_component
Module neighborhood information for RSP_2397

RSP_2397 has total of 44 gene neighbors in modules 70, 291
Gene neighbors (44)
Gene Common Name Description Module membership
RSP_0087 RSP_0087 two component transcriptional regulator, LuxR (NCBI) 70, 81
RSP_0097 smoM TRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM (NCBI) 291, 369
RSP_0099 RSP_0099 TRAP-T family sorbitol/mannitol transporter, DctQ (4TMs) subunit (NCBI) 291, 363
RSP_0161 RSP_0161 Spermidine/putrescine-binding periplasmic protein (NCBI) 70, 102
RSP_0169 RSP_0169 Na+/solute symporter (NCBI) 183, 291
RSP_0170 RSP_0170 hypothetical protein (NCBI) 174, 291
RSP_0171 RSP_0171 Response regulator receiver protein (NCBI) 178, 291
RSP_0179 RSP_0179 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components TauA (NCBI) 70, 204
RSP_0345 RSP_0345 Possible ABC transporter, periplasmic binding protein (NCBI) 70, 204
RSP_0346 RSP_0346 ABC transporter, substrate binding protein (NCBI) 70, 204
RSP_0576 RSP_0576 Na+/solute symporter (NCBI) 86, 291
RSP_0577 RSP_0577 hypothetical protein (NCBI) 86, 291
RSP_1413 RSP_1413 TRAP-T family transporter, periplasmic binding component (NCBI) 70, 102
RSP_1613 RSP_1613 TRAP-T family transporter, DctP subunit (NCBI) 25, 291
RSP_1747 bztA ABC glutamate/glutamine/aspartate/asparagine transporter, periplasmic substrate-binding protein (NCBI) 70, 102
RSP_1748 bztB ABC glutamate/glutamine/aspartate/asparagine transporter, inner membrane subunit BztB (NCBI) 70, 204
RSP_1749 bztC ABC glutamate/glutamine/aspartate/asparagine transporter, inner membrane subunit BztC (NCBI) 70, 204
RSP_1750 bztD ABC glutamate/glutamine/aspartate/asparagine transporter, ATPase subunit bztD (NCBI) 70, 204
RSP_1882 RSP_1882 ABC polyamine/opine transporter, ATPase subunit (NCBI) 70, 204
RSP_1883 RSP_1883 ABC polyamine/opine transporter, periplasmic substrate-binding protein (NCBI) 70, 204
RSP_1884 RSP_1884 ABC polyamine/opine transporter, inner membrane subunit (NCBI) 70, 204
RSP_1886 RSP_1886 ABC polyamine/opine transporter, inner membrane subunit (NCBI) 70, 204
RSP_2179 proV ABC glycine betaine/L-proline tranporter, ATPase subunit, ProV (NCBI) 70, 204
RSP_2180 proW ABC glycine betaine/L-proline transporter, inner membrane subunit (NCBI) 70, 204
RSP_2181 proX ABC glycine betaine/L-proline transporter, periplasmic substrate-binding subunit (NCBI) 52, 70
RSP_2211 RSP_2211 ABC transporter, periplasmic substrate-binding protein (NCBI) 67, 70
RSP_2320 RSP_2320 TRAP-T family transporter, periplasmic binding protein (NCBI) 16, 70
RSP_2397 RSP_2397 ABC putrescine transporter, periplasmic substrate-binding subunit (NCBI) 70, 291
RSP_2398 RSP_2398 ABC putrescine transporter, inner membrane subunit (NCBI) 174, 291
RSP_2399 RSP_2399 ABC putrescine transporter, inner membrane subunit (NCBI) 127, 291
RSP_2541 tatC twin-arginine translocation system protein, TatC (NCBI) 67, 291
RSP_2923 RSP_2923 ABC branched amino acid transporter family, periplasmic substrate-binding protein (NCBI) 70, 195
RSP_3553 dnaE DNA polymerase III alpha chain (NCBI) 291, 381
RSP_3554 xdhA xanthine dehydrogenase, small subunit (NCBI) 145, 291
RSP_3555 xdhB xanthine dehydrogenase, large subunit (NCBI) 145, 291
RSP_3556 xdhC xanthine dehydrogenase chaperone/MPT insertion protein (NCBI) 145, 291
RSP_3557 RSP_3557 ABC transporter, fused ATPase domains (NCBI) 145, 291
RSP_3558 RSP_3558 ABC transporter, inner membrane subunit (NCBI) 145, 291
RSP_3559 RSP_3559 ABC transporter, inner membrane subunit (NCBI) 145, 291
RSP_3560 RSP_3560 Possible ABC transporter, periplasmic binding protein (NCBI) 145, 291
RSP_4049 pdhAb Pyruvate dehydrogenase E1 component, beta subunit (NCBI) 25, 291
RSP_4050 pdhB Dihydrolipoamide acetyltransferase component (E2) of pyruvate dehydrogenase complex (NCBI) 25, 291
RSP_6136 RSP_6136 hypothetical protein (NCBI) 243, 291
RSP_6192 RSP_6192 hypothetical protein (NCBI) 194, 291
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_2397
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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