Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3064

transcriptional regulator, DeoR family (NCBI)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators of sugar metabolism cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3064
(Mouseover regulator name to see its description)

RSP_3064 is regulated by 22 influences and regulates 16 modules.
Regulators for RSP_3064 (22)
Regulator Module Operator
RSP_1077 235 tf
RSP_1231 235 tf
RSP_1607 235 tf
RSP_1660 235 tf
RSP_3064 235 tf
RSP_3179 235 tf
RSP_3238 235 tf
RSP_3418 235 tf
RSP_3464 235 tf
RSP_3676 235 tf
RSP_3684 235 tf
RSP_0282 292 tf
RSP_0607 292 tf
RSP_1014 292 tf
RSP_1231 292 tf
RSP_1660 292 tf
RSP_1785 292 tf
RSP_1790 292 tf
RSP_2867 292 tf
RSP_3064 292 tf
RSP_3238 292 tf
RSP_3464 292 tf

Warning: RSP_3064 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
8188 8.60e-02 agtatcTgCtTgaGctt
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8189 4.00e+02 GttcGcgCAcaAtctCGcGAcGA
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8298 6.00e+02 cCgaGaTCGAG
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8299 4.30e+02 agAagaagaagCgcaacCaGa
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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_3064

RSP_3064 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators of sugar metabolism cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for RSP_3064

RSP_3064 has total of 54 gene neighbors in modules 235, 292
Gene neighbors (54)
Gene Common Name Description Module membership
RSP_0206 RSP_0206 hypothetical protein (NCBI) 235, 303
RSP_0234 tlpL TlpL, putative cytoplasmic chemoreceptor (NCBI) 138, 235
RSP_0494 hypF hydrogenase maturation factor F (NCBI) 292, 337
RSP_1115 RSP_1115 hypothetical protein (NCBI) 246, 292
RSP_1118 RSP_1118 group 1 glycosyltransferase (NCBI) 246, 292
RSP_1332 RSP_1332 H+-transporting two-sector ATPase, alpha/beta subunit (NCBI) 235, 359
RSP_1450 RSP_1450 Inositol monophosphatase family protein (NCBI) 105, 292
RSP_1501 RSP_1501 Antisigma-factor antagonist (STAS) domain protein (NCBI) 74, 292
RSP_1509 RSP_1509 Glycoprotease (M22) metalloprotease (NCBI) 292, 300
RSP_1619 RSP_1619 hypothetical protein (NCBI) 189, 235
RSP_1620 RSP_1620 hypothetical protein (NCBI) 235, 342
RSP_1661 RSP_1661 hypothetical protein (NCBI) 292, 300
RSP_1782 RSP_1782 hypothetical membrane protein (NCBI) 233, 235
RSP_1783 RSP_1783 Predicted membrane protein (NCBI) 233, 235
RSP_1923 bioB Biotin synthase (NCBI) 62, 292
RSP_1957 RSP_1957 hypothetical protein (NCBI) 138, 235
RSP_1961 RSP_1961 hypothetical protein (NCBI) 235, 355
RSP_2034 RSP_2034 possible CAAX amino terminal protease family (NCBI) 235, 380
RSP_2040 RSP_2040 possible Transposase fragment (NCBI) 138, 235
RSP_2043 RSP_2043 hypothetical protein (NCBI) 235, 380
RSP_2061 RSP_2061 hypothetical protein (NCBI) 292, 379
RSP_2068 RSP_2068 putative ClpP-like protease (NCBI) 235, 304
RSP_2315 RSP_2315 hypothetical protein (NCBI) 105, 292
RSP_2466 RSP_2466 hypothetical protein (NCBI) 193, 235
RSP_2471 RSP_2471 Predicted phage phi-C31 gp36 major capsid-like protein (NCBI) 193, 235
RSP_2472 RSP_2472 hypothetical protein (NCBI) 193, 235
RSP_2478 RSP_2478 hypothetical protein (NCBI) 193, 235
RSP_2479 RSP_2479 putative phage host specificity protein (NCBI) 235, 320
RSP_2480 RSP_2480 hypothetical protein (NCBI) 193, 235
RSP_2501 RSP_2501 hypothetical protein (NCBI) 238, 292
RSP_2732 RSP_2732 Major facilitator superfamily (MFS) transporter (NCBI) 68, 292
RSP_2867 rpoN4 Sigma-54 factor family protein (NCBI) 282, 292
RSP_2871 aglG ABC alpha-glucoside transporter, inner membrane subunit AglG (NCBI) 229, 235
RSP_2930 RSP_2930 hypothetical protein (NCBI) 235, 238
RSP_2990 RSP_2990 hypothetical protein (NCBI) 235, 380
RSP_2996 RSP_2996 putative prohead protease (NCBI) 14, 235
RSP_2997 RSP_2997 putative head portal protein (NCBI) 14, 235
RSP_3064 RSP_3064 transcriptional regulator, DeoR family (NCBI) 235, 292
RSP_3108 RSP_3108 Putative methyl accepting chemotaxis protein (NCBI) 246, 292
RSP_3128 RSP_3128 hypothetical protein (NCBI) 292, 337
RSP_3135 RSP_3135 ppkA-related protein (NCBI) 244, 292
RSP_3201 RSP_3201 putative oxidoreductase (NCBI) 138, 235
RSP_3390 RSP_3390 ABC Fe3+-siderophores transporter, ATPase subunit (NCBI) 146, 235
RSP_3417 RSP_3417 TonB dependent outer membrane ferrichrome-iron receptor (NCBI) 235, 380
RSP_3471 RSP_3471 hypothetical protein (NCBI) 147, 292
RSP_3613 RSP_3613 Glycosyltransferase (NCBI) 238, 292
RSP_3624 RSP_3624 hypothetical protein (NCBI) 235, 307
RSP_3654 RSP_3654 None 193, 292
RSP_3684 solR transcriptional regulator, LuxR family (NCBI) 116, 235
RSP_3743 speB1 putative agmatinase (NCBI) 61, 292
RSP_3746 RSP_3746 hypothetical protein (NCBI) 61, 292
RSP_3764 RSP_3764 hypothetical protein (NCBI) 292, 347
RSP_3780 RSP_3780 hypothetical protein (NCBI) 147, 292
RSP_3789 RSP_3789 hypothetical protein (NCBI) 88, 292
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_3064
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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