Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0017

ABC spermidine/putrescine transporter, inner membrane subunit (NCBI)

CircVis
Functional Annotations (4)
Function System
ABC-type spermidine/putrescine transport system, permease component I 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_0017
(Mouseover regulator name to see its description)

RSP_0017 is regulated by 33 influences and regulates 0 modules.
Regulators for RSP_0017 (33)
Regulator Module Operator
RSP_0032 262 tf
RSP_0316 262 tf
RSP_0394 262 tf
RSP_0698 262 tf
RSP_1139 262 tf
RSP_1231 262 tf
RSP_1663 262 tf
RSP_1890 262 tf
RSP_2610 262 tf
RSP_2853 262 tf
RSP_2922 262 tf
RSP_0014 223 tf
RSP_0087 223 tf
RSP_0122 223 tf
RSP_0327 223 tf
RSP_0394 223 tf
RSP_0591 223 tf
RSP_0698 223 tf
RSP_0755 223 tf
RSP_1231 223 tf
RSP_1550 223 tf
RSP_1590 223 tf
RSP_1663 223 tf
RSP_1871 223 tf
RSP_2425 223 tf
RSP_2591 223 tf
RSP_2610 223 tf
RSP_2853 223 tf
RSP_3022 223 tf
RSP_3055 223 tf
RSP_3124 223 tf
RSP_3309 223 tf
RSP_3385 223 tf

Warning: RSP_0017 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
8164 4.90e-02 gttgGGgcAAa.Tg
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8165 7.00e+00 tTCaaTGcGGCtcaTCTaTCGCaa
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8242 3.40e+03 AAAACcctggCttT
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8243 3.70e+04 AACAGAAA
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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_0017

RSP_0017 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
ABC-type spermidine/putrescine transport system, permease component I cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
Module neighborhood information for RSP_0017

RSP_0017 has total of 53 gene neighbors in modules 223, 262
Gene neighbors (53)
Gene Common Name Description Module membership
RSP_0016 RSP_0016 ABC spermidine/putrescine transporter, inner membrane subunit (NCBI) 204, 223
RSP_0017 RSP_0017 ABC spermidine/putrescine transporter, inner membrane subunit (NCBI) 223, 262
RSP_0137 RSP_0137 hypothetical protein (NCBI) 223, 317
RSP_0167 RSP_0167 hypothetical protein (NCBI) 52, 262
RSP_0237 argE acetylornithine deacetylase (NCBI) 248, 262
RSP_0243 RSP_0243 putative lipoprotein (NCBI) 162, 262
RSP_0251 RSP_0251 Outer membrane efflux protein (NCBI) 223, 278
RSP_0252 RSP_0252 Protein-L-isoaspartatecarboxylmethyltransferase (NCBI) 262, 278
RSP_0668 RSP_0668 OmpA/MotB family protein (NCBI) 20, 262
RSP_0698 fnrL Crp-Fnr regulatory protein (FnrL) (NCBI) 200, 262
RSP_0759 RSP_0759 putative capsule polysaccharide exporter (NCBI) 223, 349
RSP_0839 RSP_0839 Predicted secreted periplasmic protein (NCBI) 262, 349
RSP_0932 ctpA Peptidase family S41 (NCBI) 51, 262
RSP_1097 RSP_1097 putative zinc protease (NCBI) 262, 308
RSP_1098 RSP_1098 hypothetical protein (NCBI) 240, 262
RSP_1126 rnr Exoribonuclease R (NCBI) 127, 262
RSP_1199 RSP_1199 secreted conserved hypothetical protein (NCBI) 200, 262
RSP_1345 RSP_1345 hypothetical protein (NCBI) 25, 262
RSP_1399 RSP_1399 hypothetical protein (NCBI) 162, 262
RSP_1430 RSP_1430 hypothetical protein (NCBI) 127, 223
RSP_1464 RSP_1464 putative periplasmic thiol-disulphide interchange protein (DsbA family) (NCBI) 262, 306
RSP_1465 RSP_1465 hypothetical protein (NCBI) 262, 306
RSP_1681 RSP_1681 two-component transcriptional regulator, winged helix family (NCBI) 223, 341
RSP_1682 RSP_1682 Two-component sensor histidine kinase (NCBI) 223, 341
RSP_1684 RSP_1684 P-loop ATPase (NCBI) 223, 341
RSP_1685 RSP_1685 PTS system, IIA component (NCBI) 223, 341
RSP_2131 rne Ribonuclease E (NCBI) 25, 223
RSP_2136 RSP_2136 hypothetical protein (NCBI) 35, 262
RSP_2167 RSP_2167 hypothetical protein (NCBI) 97, 262
RSP_2173 RSP_2173 hypothetical protein (NCBI) 127, 223
RSP_2174 RSP_2174 Putative ABC transporter, inner membrane subunit (NCBI) 127, 223
RSP_2215 RSP_2215 hypothetical protein (NCBI) 223, 323
RSP_2309 RSP_2309 hypothetical protein (NCBI) 127, 262
RSP_2419 RSP_2419 hypothetical protein (NCBI) 162, 223
RSP_2549 exoQ putative polysaccharide polymerase (NCBI) 195, 262
RSP_2550 exoK endo-beta-1,3-1,4-glycanase protein (NCBI) 200, 262
RSP_2565 ugpG UDPG-pyrophosphorylase (NCBI) 200, 223
RSP_2616 RSP_2616 hypothetical protein (NCBI) 223, 240
RSP_2633 ccmF Cytochrome c maturation protein, CcmF (NCBI) 195, 262
RSP_2653 RSP_2653 ATPase, AAA family (NCBI) 223, 345
RSP_2654 RSP_2654 DnaK suppressor protein, DksA family (NCBI) 223, 345
RSP_2682 fabD Malonyl-CoA-acyl carrier protein transacylase (NCBI) 262, 349
RSP_2771 RSP_2771 putative Exopolyphosphatase (NCBI) 262, 308
RSP_2775 lpxD UDP-3-O-(3-hydroxymyristoyl) glucosamine N-acyltransferase (NCBI) 127, 223
RSP_2900 RSP_2900 Predicted permease (NCBI) 127, 223
RSP_2901 RSP_2901 putative permease (NCBI) 223, 318
RSP_2903 RSP_2903 Probable PpiC-type peptidyl-prolyl cis-trans isomerase (NCBI) 107, 223
RSP_2947 RSP_2947 Glutamate racemase (NCBI) 127, 223
RSP_2948 RSP_2948 Putative Pyruvate ferredoxin/flavodoxin oxidoreductase (NCBI) 64, 223
RSP_2960 RSP_2960 pantetheine-phosphate adenylyltransferase (NCBI) 223, 240
RSP_2962 RSP_2962 Methylmalonic acid semialdehyde dehydrogenase (NCBI) 52, 262
RSP_2967 RSP_2967 Probable transporter, Major facilitator superfamily (MFS) (NCBI) 195, 262
RSP_3229 RSP_3229 Membrane-bound lytic murein transglycosylase B (NCBI) 200, 262
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_0017
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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