Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3518

ABC polyamine/opine transporter, inner membrane subunit (NCBI)

CircVis
Functional Annotations (4)
Function System
ABC-type spermidine/putrescine transport system, permease component II cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3518
(Mouseover regulator name to see its description)

RSP_3518 is regulated by 20 influences and regulates 0 modules.
Regulators for RSP_3518 (20)
Regulator Module Operator
RSP_1077 31 tf
RSP_1231 31 tf
RSP_1518 31 tf
RSP_1660 31 tf
RSP_1867 31 tf
RSP_2867 31 tf
RSP_3339 31 tf
RSP_3400 31 tf
RSP_3464 31 tf
RSP_3616 31 tf
RSP_3694 31 tf
RSP_0386 342 tf
RSP_1518 342 tf
RSP_1607 342 tf
RSP_2867 342 tf
RSP_3064 342 tf
RSP_3238 342 tf
RSP_3322 342 tf
RSP_3445 342 tf
RSP_3464 342 tf

Warning: RSP_3518 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
7782 2.30e-14 CgccatCCcGaTcAtcatgaC
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7783 4.50e-11 GACCcGgCCGCCccCGGcCGGgc
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8386 2.60e-02 tctcCtTaggTCgcAtTtTtT
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8387 1.90e+00 TctggcgGaAagg.cttac.gAac
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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_3518

RSP_3518 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
ABC-type spermidine/putrescine transport system, permease component II cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
Module neighborhood information for RSP_3518

RSP_3518 has total of 54 gene neighbors in modules 31, 342
Gene neighbors (54)
Gene Common Name Description Module membership
RSP_0181 RSP_0181 ABC nitrate/sulfonate/bicarbonate transporter, inner membrane subunit (NCBI) 193, 342
RSP_0221 RSP_0221 plasma membrane H+-transporting two-sector ATPase, C subunit (NCBI) 14, 342
RSP_0514 RSP_0514 dTDP-glucose 4,6-dehydratase protein (NCBI) 31, 217
RSP_0620 RSP_0620 hypothetical protein (NCBI) 313, 342
RSP_0838 RSP_0838 putative DNA polymerase III, delta subunit / DNA binding (NCBI) 141, 342
RSP_1302 motB putative chemotaxis MotB protein (NCBI) 31, 246
RSP_1307 flgI putative flagellar P-ring protein (NCBI) 31, 246
RSP_1320 flhA Flagellar biosynthesis pathway, component FlhA (NCBI) 220, 342
RSP_1333 RSP_1333 hypothetical protein (NCBI) 320, 342
RSP_1334 RSP_1334 possible chemotactic signal-response protein CheL (NCBI) 320, 342
RSP_1335 RSP_1335 hypothetical protein (NCBI) 320, 342
RSP_1336 RSP_1336 Possible FlgD protein (NCBI) 320, 342
RSP_1393 thiQ ABC thiamine transporter, ATPase subunit (NCBI) 31, 157
RSP_1456 RSP_1456 hypothetical protein (NCBI) 31, 105
RSP_1616 RSP_1616 hypothetical protein (NCBI) 141, 342
RSP_1620 RSP_1620 hypothetical protein (NCBI) 235, 342
RSP_1630 RSP_1630 hypothetical protein (NCBI) 31, 246
RSP_1635 RSP_1635 hypothetical protein (NCBI) 31, 54
RSP_1636 RSP_1636 phage-related protein, probable phage tail tape meausure protein, lambda family (NCBI) 31, 77
RSP_1656 RSP_1656 hypothetical protein (NCBI) 325, 342
RSP_1658 RSP_1658 hypothetical protein (NCBI) 325, 342
RSP_1659 RSP_1659 hypothetical protein (NCBI) 325, 342
RSP_2054 RSP_2054 hypothetical protein (NCBI) 31, 94
RSP_2058 RSP_2058 hypothetical protein (NCBI) 31, 288
RSP_2059 RSP_2059 Potential phage tail tape measure protein (NCBI) 31, 238
RSP_2260 ydjG hypothetical protein (NCBI) 267, 342
RSP_2432 RSP_2432 hypothetical protein (NCBI) 31, 370
RSP_2434 cheR1 Putative MCP methyltransferase, CheR1 (NCBI) 31, 370
RSP_2435 cheW1 Putative chemotaxis scaffold protein, CheW1 (NCBI) 31, 370
RSP_2436 cheA1 Chemotaxis histidine protein kinase, CheA1 (NCBI) 31, 370
RSP_2437 cheY1 chemotaxis response regulator, CheY1 (NCBI) 31, 370
RSP_2438 cheX Putative CheX protein (NCBI) 31, 370
RSP_2439 cheD putative chemotaxis protein, CheD (NCBI) 31, 370
RSP_2440 mcpA Methyl accepting chemotaxis protein (NCBI) 31, 370
RSP_3057 RSP_3057 ABC proline/glycine betaine transporter, ATPase subunit (NCBI) 105, 342
RSP_3058 RSP_3058 ABC proline/glycine betaine transporter, inner membrane subunit (NCBI) 105, 342
RSP_3059 RSP_3059 ABC proline/glycine betaine transporter, periplasmic substrate-binding protein (NCBI) 105, 342
RSP_3110 RSP_3110 Putative Glutathione S-transferase (NCBI) 62, 342
RSP_3360 RSP_3360 Adenine specific DNA methyltransferase, D12 class (NCBI) 103, 342
RSP_3406 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase 2 (NCBI) 61, 342
RSP_3445 RSP_3445 transcriptional regulator, GntR family (NCBI) 61, 342
RSP_3516 RSP_3516 ABC polyamine/opine transporter, ATPase subunit (NCBI) 31, 282
RSP_3518 RSP_3518 ABC polyamine/opine transporter, inner membrane subunit (NCBI) 31, 342
RSP_3544 RSP_3544 hypothetical protein (NCBI) 14, 342
RSP_3545 RSP_3545 hypothetical protein (NCBI) 325, 342
RSP_3632 RSP_3632 hypothetical protein (NCBI) 31, 94
RSP_3656 RSP_3656 NAD-dependent aldehyde dehydrogenases (NCBI) 31, 105
RSP_3661 RSP_3661 TRAP-T family transporter, periplasmic binding protein (NCBI) 208, 342
RSP_3662 RSP_3662 TRAP-T family transporter, large (12TMs) inner membrane subunit (NCBI) 208, 342
RSP_3663 RSP_3663 TRAP-T family transporter, small (4TMs) inner membrane subunit (NCBI) 141, 342
RSP_3690 RSP_3690 resiniferatoxin-binding, phosphotriesterase-related protein (NCBI) 31, 253
RSP_3691 RSP_3691 putative cytoplasmic protein (NCBI) 31, 57
RSP_3767 RSP_3767 hypothetical protein (NCBI) 31, 150
RSP_3781 RSP_3781 putative phage terminase large subunit (NCBI) 150, 342
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_3518
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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