Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3089

hypothetical protein (NCBI)

CircVis
Functional Annotations (3)
Function System
Uncharacterized conserved protein cog/ cog
metabolic process go/ biological_process
carbon-sulfur lyase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3089
(Mouseover regulator name to see its description)

RSP_3089 is regulated by 30 influences and regulates 0 modules.
Regulators for RSP_3089 (30)
Regulator Module Operator
RSP_0014 231 tf
RSP_0071 231 tf
RSP_0395 231 tf
RSP_0601 231 tf
RSP_0641 231 tf
RSP_0755 231 tf
RSP_1191 231 tf
RSP_1274 231 tf
RSP_1518 231 tf
RSP_1776 231 tf
RSP_1915 231 tf
RSP_2026 231 tf
RSP_2324 231 tf
RSP_2719 231 tf
RSP_2840 231 tf
RSP_2850 231 tf
RSP_2965 231 tf
RSP_3324 231 tf
RSP_3667 231 tf
RSP_0014 210 tf
RSP_0601 210 tf
RSP_0641 210 tf
RSP_1191 210 tf
RSP_1274 210 tf
RSP_1518 210 tf
RSP_1776 210 tf
RSP_1866 210 tf
RSP_2965 210 tf
RSP_3324 210 tf
RSP_3667 210 tf

Warning: RSP_3089 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
8140 1.20e+03 CGAtCttC.CCtc
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8141 1.50e+04 GGCAGA
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8180 6.70e+00 gaaAggcCa.GgaGa
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8181 5.70e+03 GgA.gctcccgcaGCAGGAgGag
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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_3089

RSP_3089 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Uncharacterized conserved protein cog/ cog
metabolic process go/ biological_process
carbon-sulfur lyase activity go/ molecular_function
Module neighborhood information for RSP_3089

RSP_3089 has total of 34 gene neighbors in modules 210, 231
Gene neighbors (34)
Gene Common Name Description Module membership
RSP_0370 RSP_0370 hypothetical protein (NCBI) 210, 327
RSP_1025 RSP_1025 hypothetical protein (NCBI) 210, 231
RSP_1026 RSP_1026 hypothetical protein (NCBI) 210, 231
RSP_1053 ffh Signal recognition particle protein ffh (NCBI) 210, 277
RSP_1127 ElaA acetyltransferase, GNAT family (NCBI) 214, 231
RSP_1146 gltB Glutamine-pyruvate aminotransferase (NCBI) 231, 271
RSP_1147 RSP_1147 hypothetical protein (NCBI) 210, 231
RSP_1148 RSP_1148 hypothetical protein (NCBI) 210, 231
RSP_1258 RSP_1258 putative hydrolase (NCBI) 231, 280
RSP_1490 RSP_1490 Putative ATP-dependent protease La, LON (NCBI) 231, 372
RSP_1491 RSP_1491 hypothetical protein (NCBI) 210, 231
RSP_1542 RSP_1542 ABC transporter, ATPase subunit (NCBI) 210, 286
RSP_1591 RSP_1591 Predicted Glutathione S-transferase (NCBI) 210, 231
RSP_1692 pduO hypothetical protein (NCBI) 58, 231
RSP_1895 RSP_1895 Small-conductance mechanosensitive ion channel (NCBI) 91, 231
RSP_2128 purQ phosphoribosylformylglycinamidine synthase I (FGAM) synthase (NCBI) 58, 231
RSP_2268 RSP_2268 metallo Beta lactamase superfamily (NCBI) 210, 231
RSP_2312 RSP_2312 hypothetical protein (NCBI) 215, 231
RSP_2314 RSP_2314 oxidoreductase, Chromogranin/secretogranin (NCBI) 158, 231
RSP_2388 RSP_2388 hypothetical protein (NCBI) 161, 210
RSP_2389 RSP_2389 putative glutathione peroxidase (NCBI) 210, 231
RSP_2645 eda KDPG/KHG bifunctional aldolase (NCBI) 231, 301
RSP_2970 RSP_2970 Transporter, Major facilitator superfamily (MFS) (NCBI) 231, 356
RSP_3075 RSP_3075 hypothetical protein (NCBI) 210, 231
RSP_3076 RSP_3076 hypothetical protein (NCBI) 210, 231
RSP_3089 RSP_3089 hypothetical protein (NCBI) 210, 231
RSP_3138 RSP_3138 Smp-30/Cgr1 family protein (NCBI) 210, 280
RSP_3162 RSP_3162 hypothetical protein (NCBI) 58, 231
RSP_3163 RSP_3163 Probable oxidoreductase (NCBI) 58, 231
RSP_3164 RSP_3164 ferredoxin like protein (NCBI) 58, 231
RSP_3272 ggt Gamma-glutamyltranspeptidase (NCBI) 210, 239
RSP_3310 RSP_3310 None 158, 210
RSP_3351 RSP_3351 hypothetical protein (NCBI) 210, 231
RSP_3537 RSP_3537 alcohol dehydrogenase, zinc-containing (NCBI) 210, 231
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_3089
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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