Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3174

Nucleoside transporter, NCS1 family (NCBI)

CircVis
Functional Annotations (4)
Function System
Cytosine/uracil/thiamine/allantoin permeases cog/ cog
nucleobase transmembrane transporter activity go/ molecular_function
nucleobase-containing compound transport go/ biological_process
membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3174
(Mouseover regulator name to see its description)

RSP_3174 is regulated by 27 influences and regulates 0 modules.
Regulators for RSP_3174 (27)
Regulator Module Operator
RSP_0394 160 tf
RSP_0395 160 tf
RSP_0457 160 tf
RSP_0728 160 tf
RSP_0794 160 tf
RSP_1139 160 tf
RSP_1231 160 tf
RSP_1272 160 tf
RSP_1704 160 tf
RSP_1936 160 tf
RSP_2324 160 tf
RSP_2533 160 tf
RSP_2801 160 tf
RSP_2850 160 tf
RSP_2888 160 tf
RSP_2922 160 tf
RSP_3022 160 tf
RSP_3448 160 tf
RSP_0068 281 tf
RSP_0186 281 tf
RSP_0591 281 tf
RSP_0927 281 tf
RSP_1231 281 tf
RSP_1936 281 tf
RSP_2351 281 tf
RSP_2801 281 tf
RSP_3203 281 tf

Warning: RSP_3174 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
8040 3.20e-03 cTTGaCC.t.G
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8041 1.40e+01 CtTGCcTaTGGAGagGGcGCTTTG
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8276 2.60e+03 CaTaCattTt
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8277 5.80e+03 AAGGTCAAT
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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_3174

RSP_3174 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Cytosine/uracil/thiamine/allantoin permeases cog/ cog
nucleobase transmembrane transporter activity go/ molecular_function
nucleobase-containing compound transport go/ biological_process
membrane go/ cellular_component
Module neighborhood information for RSP_3174

RSP_3174 has total of 29 gene neighbors in modules 160, 281
Gene neighbors (29)
Gene Common Name Description Module membership
RSP_0218 mcpM methyl accepting chemotaxis protein (NCBI) 281, 306
RSP_0246 RSP_0246 ABC lipid efflux transporter, fused ATPase and inner membrane subunits (NCBI) 281, 317
RSP_0414 RSP_0414 hypothetical protein (NCBI) 124, 281
RSP_0588 RSP_0588 hypothetical protein (NCBI) 96, 160
RSP_0998 nhaD Na+/H+ antiporter, NhaD (NCBI) 160, 268
RSP_1296 nagA putative N-acetylglucosamine-6-phosphate deacetylase (NCBI) 281, 303
RSP_1349 RSP_1349 hypothetical protein (NCBI) 160, 362
RSP_1571 purE Phosphoribosylaminoimidazole carboxylase, catalytic subunit (NCBI) 108, 160
RSP_1696 RSP_1696 DNA topoisomerase IV, A subunit (NCBI) 160, 224
RSP_1744 RSP_1744 CrcB-like protein (NCBI) 160, 361
RSP_1745 RSP_1745 Pseudouridine synthase (NCBI) 160, 361
RSP_1847 PurD Phosphoribosylamine--glycine ligase (NCBI) 160, 356
RSP_1855 RSP_1855 hypothetical protein (NCBI) 160, 258
RSP_1857 RSP_1857 hypothetical protein (NCBI) 160, 258
RSP_1858 glyS Glycyl-tRNA synthetase, beta subunit (NCBI) 160, 258
RSP_1989 valS Putative valyl-tRNA synthetase (NCBI) 160, 203
RSP_2243 hisA phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (NCBI) 160, 258
RSP_2712 fabZ probable 3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratase (NCBI) 113, 281
RSP_2714 lpxA Acyl-(acyl carrier protein))-UDP-N-acetylglucosamine O-acyltransferase (NCBI) 268, 281
RSP_2786 HPRT Hypoxanthine-guanine phosphoribosyltransferase (NCBI) 281, 318
RSP_2872 aglF ABC alpha-glucoside transporter, inner membrane subunit AglF (NCBI) 281, 307
RSP_2875 glk putative glucokinase (NCBI) 160, 258
RSP_2895 RSP_2895 putative ABC transporter, fused ATPase subunits (NCBI) 15, 160
RSP_2943 argS Arginyl-tRNA synthetase, class I (NCBI) 160, 372
RSP_2980 aspAT Putative aspartate aminotransferase A (NCBI) 281, 311
RSP_3080 RSP_3080 Choline/carnitine/betaine transporter, BCCT family (NCBI) 160, 203
RSP_3174 RSP_3174 Nucleoside transporter, NCS1 family (NCBI) 160, 281
RSP_3549 hisG ATP phosphoribosyltransferase (NCBI) 160, 268
RSP_3551 hisS Histidyl-tRNA synthetase (NCBI) 160, 258
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_3174
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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