Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3317

transcriptional regulator, TetR family (NCBI)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3317
(Mouseover regulator name to see its description)

RSP_3317 is regulated by 16 influences and regulates 12 modules.
Regulators for RSP_3317 (16)
Regulator Module Operator
RSP_0087 316 tf
RSP_0623 316 tf
RSP_1139 316 tf
RSP_1220 316 tf
RSP_1518 316 tf
RSP_2324 316 tf
RSP_2610 316 tf
RSP_3238 316 tf
RSP_3317 316 tf
RSP_0185 247 tf
RSP_0386 247 tf
RSP_1590 247 tf
RSP_1660 247 tf
RSP_1871 247 tf
RSP_3317 247 tf
RSP_3339 247 tf

Warning: RSP_3317 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
8212 5.40e+03 ttCTGcCGGGccGcCtGccC
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8213 2.60e+04 TTCGAT
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8344 6.30e-03 AtAATATT
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8345 6.00e-01 aagCCagAACAAgtAgCacAG
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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_3317

RSP_3317 is enriched for 5 functions in 3 categories.
Module neighborhood information for RSP_3317

RSP_3317 has total of 26 gene neighbors in modules 247, 316
Gene neighbors (26)
Gene Common Name Description Module membership
RSP_0425 metG Methionyl-tRNA synthetase (NCBI) 311, 316
RSP_0478 RSP_0478 putative lysyl-tRNA synthetase (NCBI) 183, 316
RSP_0567 RSP_0567 Probable Methylated-DNA-(protein)-cysteine S-methyltransferase (NCBI) 316, 337
RSP_0819 rhlE2 DEAD/DEAH box helicase (NCBI) 209, 316
RSP_0945 RSP_0945 Major facilitator superfamily (MFS) transporter (NCBI) 19, 247
RSP_1128 dapE succinyl-diaminopimelate desuccinylase (NCBI) 69, 316
RSP_1426 RSP_1426 RNA-binding region RNP-1 (NCBI) 209, 316
RSP_1427 RSP_1427 hypothetical protein (NCBI) 209, 316
RSP_1965 RSP_1965 Putative Membrane Fusion Protein Family member (NCBI) 107, 247
RSP_2254 RSP_2254 ABC efflux transporter, fused ATPase and inner membrane subunits (NCBI) 115, 316
RSP_2409 rluD putative Pseudouridine synthase, Rlu (NCBI) 54, 316
RSP_2552 exoU Glycosyl transferase, family 2 (NCBI) 209, 316
RSP_2558 RSP_2558 hypothetical protein (NCBI) 157, 316
RSP_2559 RSP_2559 ABC transporter, fused ATPase and inner membrane subunits (NCBI) 247, 288
RSP_2659 dgt Deoxyguanosinetriphosphate triphosphohydrolase (NCBI) 117, 316
RSP_3005 RSP_3005 hypothetical protein (NCBI) 40, 316
RSP_3006 RSP_3006 conserved hypothetical protein containing Von Willebrand factor, type A domain (NCBI) 40, 316
RSP_3054 RSP_3054 hypothetical protein (NCBI) 247, 331
RSP_3317 RSP_3317 transcriptional regulator, TetR family (NCBI) 247, 316
RSP_3318 acrB Cation/multidrug efflux pump, RND family (NCBI) 301, 316
RSP_3321 acrA Cation/multidrug efflux pump, membrane-fusion protein (NCBI) 301, 316
RSP_3435 RSP_3435 possible DNA-binding protein (NCBI) 91, 316
RSP_3658 hpcH putative 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (NCBI) 105, 316
RSP_3772 RSP_3772 hypothetical protein (NCBI) 247, 380
RSP_3778 RSP_3778 hypothetical protein (NCBI) 53, 247
RSP_3795 RSP_3795 hypothetical protein (NCBI) 247, 288
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_3317
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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