Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2801 tetR

transcriptional regulator, TetR family, (NCBI)

CircVis
Functional Annotations (4)
Function System
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_2801
(Mouseover regulator name to see its description)

RSP_2801 is regulated by 19 influences and regulates 19 modules.
Regulators for RSP_2801 tetR (19)
Regulator Module Operator
RSP_0415 3 tf
RSP_0507 3 tf
RSP_1139 3 tf
RSP_1272 3 tf
RSP_1274 3 tf
RSP_2130 3 tf
RSP_2801 3 tf
RSP_3094 3 tf
RSP_3665 3 tf
RSP_0122 64 tf
RSP_0316 64 tf
RSP_0794 64 tf
RSP_1139 64 tf
RSP_2200 64 tf
RSP_2425 64 tf
RSP_2610 64 tf
RSP_2801 64 tf
RSP_3238 64 tf
RSP_3694 64 tf

Warning: RSP_2801 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
7728 1.40e-03 TgttcgACTTtTcaGacG
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7729 1.70e-03 TTCtTgcga
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7848 3.00e-05 TtttTGaCTtT
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7849 1.20e-03 CG.gCAga.gGtt.cgtAaAcGAC
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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_2801

RSP_2801 is enriched for 4 functions in 2 categories.
Enrichment Table (4)
Function System
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
Module neighborhood information for RSP_2801

RSP_2801 has total of 51 gene neighbors in modules 3, 64
Gene neighbors (51)
Gene Common Name Description Module membership
RSP_0091 smoE ABC sorbitol/mannitol transporter, periplasmic binding protein (NCBI) 56, 64
RSP_0092 smoF ABC sorbitol/mannitol transporter, inner membrane subunit (NCBI) 56, 64
RSP_0093 smoG ABC sorbitol/mannitol transporter, inner membrane subunit (NCBI) 56, 64
RSP_0094 smoK ABC sorbitol/mannitol transporter, ATPase subunit (NCBI) 56, 64
RSP_0095 smoS Sorbitol dehydrogenase (NCBI) 56, 64
RSP_0096 mtlK Mannitol dehydrogenase (NCBI) 56, 64
RSP_0458 RSP_0458 hypothetical protein (NCBI) 35, 64
RSP_0557 RSP_0557 hypothetical protein (NCBI) 3, 48
RSP_0870 RSP_0870 hypothetical protein (NCBI) 3, 132
RSP_1016 RSP_1016 small heat shock protein (NCBI) 3, 132
RSP_1138 RSP_1138 two component transcriptional regulator, winged helix family (NCBI) 64, 250
RSP_1139 RSP_1139 transcriptional regulator, MarR family (NCBI) 64, 250
RSP_1140 ilvE Branched chain acid aminotransferase (NCBI) 64, 112
RSP_1193 RSP_1193 None 3, 366
RSP_1194 grxC Glutaredoxin (NCBI) 3, 366
RSP_1270 RSP_1270 hypothetical protein (NCBI) 3, 132
RSP_1271 RSP_1271 periplasmic sensor signal transduction histidine kinase (NCBI) 3, 132
RSP_1272 RSP_1272 sigma24 (NCBI) 3, 132
RSP_1273 RSP_1273 hypothetical protein (NCBI) 3, 132
RSP_1274 RSP_1274 response regulator receiver protein (NCBI) 3, 132
RSP_1531 RSP_1531 heat shock protein hslV, proteasome-related peptidase subunit (NCBI) 3, 132
RSP_1549 RSP_1549 hypothetical protein (NCBI) 3, 366
RSP_1572 RSP_1572 Heat shock protein, Hsp20 family (NCBI) 3, 132
RSP_1573 RSP_1573 hypothetical protein (NCBI) 3, 132
RSP_1679 RSP_1679 acyl-CoA dehydrogenase (NCBI) 64, 140
RSP_1840 RSP_1840 hypothetical protein (NCBI) 3, 366
RSP_1880 RSP_1880 hypothetical protein (NCBI) 64, 185
RSP_2007 RSP_2007 conservd hypothetical protein (NCBI) 64, 71
RSP_2261 ydjI Antifreeze protein, type I (NCBI) 64, 200
RSP_2265 RSP_2265 hypothetical protein (NCBI) 3, 366
RSP_2481 cysE serine acetyltransferase (NCBI) 46, 64
RSP_2590 RSP_2590 hypothetical protein (NCBI) 64, 338
RSP_2636 ilvH Acetolactate synthase, small (regulatory) subunit (NCBI) 3, 366
RSP_2637 RSP_2637 Acetolactate synthase, large subunit, biosynthetic type (NCBI) 3, 366
RSP_2657 xthA Exodeoxyribonuclease III (NCBI) 3, 132
RSP_2658 RSP_2658 HesB/YadR/YfhF family protein (NCBI) 3, 117
RSP_2718 RSP_2718 possible outer membrane protein (NCBI) 3, 309
RSP_2763 RSP_2763 hypothetical protein (NCBI) 48, 64
RSP_2801 tetR transcriptional regulator, TetR family, (NCBI) 3, 64
RSP_2802 RSP_2802 multidrug/cation efflux pump, membrane fusion protein subunit (NCBI) 3, 64
RSP_2803 RSP_2803 multidrug/cation efflux pump, RND superfamily (NCBI) 3, 64
RSP_2805 nemA Putative NADH-flavin oxidoreductase (NCBI) 3, 132
RSP_2806 lon Probable ATP-dependent protease La protein (NCBI) 3, 200
RSP_2856 RSP_2856 putative oligopeptide ABC transporter, periplasmic-binding protein (NCBI) 64, 277
RSP_2876 RSP_2876 putative carbon monoxide dehydrogenase medium chain (NCBI) 64, 338
RSP_2877 coxL Putative carbon monoxide dehydrogenase large chain (NCBI) 64, 338
RSP_2878 coxS Putative carbon-monoxide dehydrogenase small chain (NCBI) 64, 338
RSP_2879 RSP_2879 hypothetical protein (NCBI) 64, 338
RSP_2948 RSP_2948 Putative Pyruvate ferredoxin/flavodoxin oxidoreductase (NCBI) 64, 223
RSP_2982 gcpE Probable 4-hydroxy-3-methylbut-2-en-1-yl diphosphate (NCBI) 64, 185
RSP_3562 sqr sulfide-quinone reductase (NCBI) 64, 237
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_2801
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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