Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3238

hypothetical protein (NCBI)

CircVis
Functional Annotations (5)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
protein dimerization activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3238
(Mouseover regulator name to see its description)

RSP_3238 is regulated by 16 influences and regulates 64 modules.
Regulators for RSP_3238 (16)
Regulator Module Operator
RSP_0547 264 tf
RSP_1518 264 tf
RSP_2346 264 tf
RSP_2572 264 tf
RSP_3238 264 tf
RSP_3341 264 tf
RSP_0443 382 tf
RSP_0527 382 tf
RSP_0927 382 tf
RSP_2346 382 tf
RSP_2572 382 tf
RSP_2800 382 tf
RSP_2888 382 tf
RSP_2963 382 tf
RSP_3238 382 tf
RSP_3341 382 tf

Warning: RSP_3238 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
8246 3.60e-04 AaTg.taAgca.gC.TatTa.ata
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8247 4.60e+01 TcCTCacGattTcgCGcGcaGCca
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8454 2.30e-05 at.aGaaTtgATCtaaGTcaa
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8455 2.40e+02 ggcgAcAAaT
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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_3238

RSP_3238 is enriched for 5 functions in 2 categories.
Enrichment Table (5)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
protein dimerization activity go/ molecular_function
Module neighborhood information for RSP_3238

RSP_3238 has total of 39 gene neighbors in modules 264, 382
Gene neighbors (39)
Gene Common Name Description Module membership
RSP_0283 ppaA regulatory protein, PpaA (NCBI) 163, 382
RSP_0474 cycP Cytochrome c' (NCBI) 21, 264
RSP_0475 RSP_0475 cytochrome b (NCBI) 27, 264
RSP_0590 RSP_0590 hypothetical protein (NCBI) 85, 382
RSP_0697 RSP_0697 Universal stress protein (Usp) (NCBI) 305, 382
RSP_0775 RSP_0775 Class I monoheme cytochrome c (NCBI) 78, 382
RSP_0869 osp response regulator receive protein (NCBI) 257, 382
RSP_1087 RSP_1087 Short-chain dehydrogenase/reductase family member (NCBI) 49, 264
RSP_1278 cbbZ phosphoglycolate phosphatase (NCBI) 248, 264
RSP_1279 cbbY CbbY family protein (NCBI) 248, 264
RSP_1280 cbbX CbbX protein (NCBI) 144, 264
RSP_1281 cbbS Ribulose bisphosphate carboxylase, small subunit (NCBI) 264, 284
RSP_1282 cbbL Ribulose bisphosphate carboxylase, large subunit, form I (NCBI) 264, 284
RSP_1283 cfxA Fructose-bisphosphate aldolase I (NCBI) 264, 284
RSP_1406 RSP_1406 hypothetical protein (NCBI) 49, 264
RSP_1508 RSP_1508 Uncharacterized HemY-like membrane protein (NCBI) 144, 382
RSP_1513 trpB Putative Tryptophan synthase beta chain (NCBI) 85, 382
RSP_1759 RSP_1759 hypothetical protein (NCBI) 144, 264
RSP_1836 apt adenine phosphoribosyltransferase (NCBI) 45, 382
RSP_1837 RSP_1837 Purine nucleoside phosphorylase, probable 5'-methylthioadenosine phosphorylase (NCBI) 45, 382
RSP_2085 RSP_2085 hypothetical protein (NCBI) 49, 382
RSP_2086 RSP_2086 Putative Antibiotic biosynthesis monooxygenase (NCBI) 45, 264
RSP_2235 RSP_2235 hypothetical protein (NCBI) 264, 365
RSP_2236 RSP_2236 transcriptional regulator, MarR family (NCBI) 264, 365
RSP_2237 RSP_2237 Membrane Fusion Protein (MFP) Family protein (NCBI) 264, 365
RSP_2238 RSP_2238 multidrug efflux pump, Major facilitator superfamily (MFS) (NCBI) 264, 365
RSP_2247 fusA putative translation elongation factor (NCBI) 78, 382
RSP_2337 RSP_2337 hypothetical protein (NCBI) 78, 382
RSP_2386 RSP_2386 translation initiation factor eIF-2B, alpha subunit (NCBI) 45, 382
RSP_2394 kdtA putative 3-deoxy-D-manno-octulosonic-acid transferase (KDO transferase) (NCBI) 305, 382
RSP_2395 RSP_2395 BCCP, cytochrome c peroxidase (NCBI) 305, 382
RSP_2656 nahG putative salicylate hydroxylase (Salicylate 1-monooxygenase) (NCBI) 144, 382
RSP_2848 hemB Delta-aminolevulinic acid dehydratase (Porphobilinogen synthase) (NCBI) 85, 382
RSP_2864 cbbE Pentose-5-phosphate-3-epimerase (NCBI) 132, 264
RSP_2888 RSP_2888 Transcriptional regulator (NCBI) 163, 382
RSP_3238 RSP_3238 hypothetical protein (NCBI) 264, 382
RSP_3265 RSP_3265 hypothetical protein (NCBI) 264, 284
RSP_3306 RSP_3306 hypothetical protein (NCBI) 144, 264
RSP_3587 RSP_3587 N-(5'-phosphoribosyl)anthranilate isomerase (NCBI) 173, 382
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_3238
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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