Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2853

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_2853
(Mouseover regulator name to see its description)

RSP_2853 is regulated by 11 influences and regulates 22 modules.
Regulators for RSP_2853 (11)
Regulator Module Operator
RSP_0071 12 tf
RSP_0981 12 tf
RSP_1274 12 tf
RSP_1518 12 tf
RSP_2362 12 tf
RSP_2681 12 tf
RSP_2853 12 tf
RSP_2922 12 tf
RSP_3324 12 tf
RSP_1790 95 tf
RSP_2730 95 tf

Warning: RSP_2853 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
7744 4.90e-06 CCGaTTGCATCGcCCGACaaGaAG
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7745 7.40e-02 aCacaacCTTGatcTTGcCtGACG
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7910 1.40e-15 tgcgCAca.Aa.GgAtccTGtcaA
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7911 2.40e-05 AAAaTtaacGaCcAAtCAATC
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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_2853

RSP_2853 is enriched for 5 functions in 3 categories.
Module neighborhood information for RSP_2853

RSP_2853 has total of 35 gene neighbors in modules 12, 95
Gene neighbors (35)
Gene Common Name Description Module membership
RSP_0182 RSP_0182 None 95, 175
RSP_0610 RSP_0610 Putative 3-oxoacyl-(acyl-carrier-protein) reductase (NCBI) 95, 273
RSP_0736 mobC MobC protein (NCBI) 12, 187
RSP_0737 mobB Molybdopterin guanine dinucleotide synthesis (NCBI) 12, 187
RSP_0738 mobA molybdopterin-guanine dinucleotide biosynthesis protein A (NCBI) 12, 187
RSP_0739 RSP_0739 Branched chain amino acid efflux pump, large (AzlC) subunit (NCBI) 12, 113
RSP_0796 cobQ cobyric acid synthase (NCBI) 95, 158
RSP_1434 RSP_1434 Putative Zn-dependent oxidoreductase (NCBI) 95, 113
RSP_1758 RSP_1758 Probable succinyl-diaminopimelate desuccinylase (NCBI) 95, 102
RSP_2632 argI Arginase (NCBI) 95, 168
RSP_2730 RSP_2730 Transcriptional regulator, ArsR family (NCBI) 67, 95
RSP_2851 RSP_2851 multidrug (bicyclomycin) efflux pump, Major facilitator superfamily (MFS) (NCBI) 12, 30
RSP_2852 RSP_2852 Predicted polyketide biosynthesis associated protein (NCBI) 12, 184
RSP_2853 RSP_2853 Transcriptional regulator, TetR family (NCBI) 12, 95
RSP_2854 RSP_2854 Cation/multidrug efflux pump, Membrane fusion protein (MFP) family (NCBI) 12, 95
RSP_2855 RSP_2855 Cation/multidrug efflux pump, RND superfamily (NCBI) 12, 95
RSP_2932 hutC Histidine utilization repressor, gntR family (NCBI) 95, 97
RSP_2933 hutF Formiminoglutamate deiminase (NCBI) 95, 97
RSP_2934 hutI Imidazolone-5-propionate hydrolase (NCBI) 95, 97
RSP_2935 hutH Probable histidine ammonia-lyase (NCBI) 95, 97
RSP_2936 hutU Urocanase (NCBI) 95, 97
RSP_3298 RSP_3298 transcriptional regulator, LysR family (NCBI) 95, 273
RSP_3403 RSP_3403 hypothetical protein (NCBI) 95, 102
RSP_3404 RSP_3404 hypothetical protein (NCBI) 95, 244
RSP_3405 gntR transcriptional regulator, GntR family (NCBI) 95, 244
RSP_3520 RSP_3520 ABC peptide transporter, fused ATPase domains (NCBI) 95, 170
RSP_3522 RSP_3522 ABC peptide transporter, inner membrane subunit (NCBI) 95, 170
RSP_3523 RSP_3523 ABC peptide transporter, inner membrane subunit (NCBI) 95, 170
RSP_3524 RSP_3524 ABC peptide transporter, periplasmic binding protein (NCBI) 95, 170
RSP_3525 RSP_3525 ABC peptide transporter, periplasmic binding protein (NCBI) 95, 170
RSP_3526 RSP_3526 Amidase (NCBI) 95, 170
RSP_3527 RSP_3527 Probable acetylpolyamine aminohydrolase (NCBI) 95, 170
RSP_3584 RSP_3584 hypothetical protein (NCBI) 95, 242
RSP_6196 RSP_6196 hypothetical protein (NCBI) 12, 321
RSP_6204 RSP_6204 hypothetical protein (NCBI) 12, 270
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_2853
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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