Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3664

transcriptional regulator, GntR family (NCBI)

CircVis
Functional Annotations (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of fatty acid metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3664
(Mouseover regulator name to see its description)

RSP_3664 is regulated by 24 influences and regulates 10 modules.
Regulators for RSP_3664 (24)
Regulator Module Operator
RSP_0090 331 tf
RSP_0443 331 tf
RSP_1225 331 tf
RSP_1590 331 tf
RSP_1892 331 tf
RSP_2351 331 tf
RSP_2533 331 tf
RSP_2780 331 tf
RSP_3179 331 tf
RSP_3339 331 tf
RSP_3514 331 tf
RSP_0774 268 tf
RSP_0907 268 tf
RSP_1163 268 tf
RSP_1191 268 tf
RSP_1231 268 tf
RSP_1739 268 tf
RSP_1741 268 tf
RSP_3124 268 tf
RSP_3179 268 tf
RSP_3309 268 tf
RSP_3664 268 tf
RSP_3676 268 tf
RSP_3686 268 tf

Warning: RSP_3664 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
8254 7.30e+01 GCccTgTCatTtG
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8255 2.80e+03 AAaCTGacaT
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8368 5.00e-18 CagaT..ataAcgttaaatCATa.
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8369 6.40e-03 GATaTGacATAaCcCattGaaTGC
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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_3664

RSP_3664 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of fatty acid metabolic process go/ biological_process
Module neighborhood information for RSP_3664

RSP_3664 has total of 46 gene neighbors in modules 268, 331
Gene neighbors (46)
Gene Common Name Description Module membership
RSP_0780 RSP_0780 hypothetical protein with ATP/GTP-binding site (NCBI) 13, 268
RSP_0848 xthA1 Exodeoxyribonuclease III (NCBI) 184, 268
RSP_0944 purU PurU, Formyltetrahydrofolate deformylase (NCBI) 124, 268
RSP_0998 nhaD Na+/H+ antiporter, NhaD (NCBI) 160, 268
RSP_1052 RSP_1052 possible Acetyltransferase (NCBI) 268, 271
RSP_1105 DapB Dihydrodipicolinate reductase (DHPR) (NCBI) 268, 299
RSP_1339 RSP_1339 Formamidopyrimidine-DNA glycolase (NCBI) 84, 331
RSP_1372 RSP_1372 Major facilitator superfamily (MFS) transporter (NCBI) 289, 331
RSP_1381 RSP_1381 hypothetical protein (NCBI) 47, 268
RSP_1382 RSP_1382 radical SAM superfamily protein (NCBI) 266, 268
RSP_1390 RSP_1390 Putative transporter, DMT superfamily (NCBI) 192, 331
RSP_1484 RSP_1484 hypothetical protein (NCBI) 209, 268
RSP_1485 RSP_1485 ATP-dependent RNA helicase (NCBI) 209, 268
RSP_1706 RSP_1706 Putative acetyltransferase (NCBI) 13, 268
RSP_1832 RSP_1832 peptidase, M16 family (NCBI) 69, 268
RSP_1892 RSP_1892 putative Cro/CI transcriptional regulator (NCBI) 313, 331
RSP_1927 RSP_1927 hypothetical protein (NCBI) 126, 331
RSP_2004 trpE Anthranilate synthase component I and chorismate binding protein (NCBI) 203, 268
RSP_2304 ribF Riboflavin kinase / FAD synthetase = FMN adenylyltransferase, RibF (NCBI) 268, 343
RSP_2358 RSP_2358 possible phage phi-C31 gp36-like protein / Major capsid protein, HK97 family (NCBI) 221, 331
RSP_2359 RSP_2359 hypothetical protein (NCBI) 161, 331
RSP_2360 RSP_2360 putative head portal protein, HK97 family (NCBI) 161, 331
RSP_2454 purF Amidophosphoribosyltransferase (NCBI) 218, 268
RSP_2714 lpxA Acyl-(acyl carrier protein))-UDP-N-acetylglucosamine O-acyltransferase (NCBI) 268, 281
RSP_2778 RSP_2778 hypothetical protein (NCBI) 224, 268
RSP_2841 trkA potassium uptake tranporter, NAD-binding subunit, TrkA (NCBI) 63, 268
RSP_2902 RSP_2902 Putative organic solvent tolerance protein (NCBI) 87, 268
RSP_2929 RSP_2929 putative disulfide bond formation protein DsbB (NCBI) 2, 331
RSP_3054 RSP_3054 hypothetical protein (NCBI) 247, 331
RSP_3073 RSP_3073 ErfK/YbiS/YcfS/YnhG family protein (NCBI) 188, 331
RSP_3117 RSP_3117 hypothetical protein (NCBI) 161, 331
RSP_3242 RSP_3242 Putative trypsin-like serine protease (NCBI) 253, 331
RSP_3329 RSP_3329 hypothetical protein (NCBI) 133, 331
RSP_3386 RSP_3386 TRAP-T family transporter, periplasmic binding protein (NCBI) 220, 331
RSP_3416 RSP_3416 ABC Fe+3-siderophore transporter, periplasmic binding protein (NCBI) 74, 331
RSP_3514 RSP_3514 transcriptional regulator, AraC family (NCBI) 288, 331
RSP_3515 RSP_3515 ABC polyamine/opine transporter, periplasmic binding protein (NCBI) 288, 331
RSP_3517 RSP_3517 ABC polyamine/opine transporter, inner membrane subunit (NCBI) 331, 379
RSP_3519 RSP_3519 putative proline racemase (NCBI) 282, 331
RSP_3549 hisG ATP phosphoribosyltransferase (NCBI) 160, 268
RSP_3550 RSP_3550 Aminoacyl-transfer RNA synthetase, class II (NCBI) 212, 268
RSP_3567 znuB ABC zinc tranporter, inner membrane subunit ZnuB (NCBI) 161, 331
RSP_3568 znuC ABC zinc transporter, ATPase subunit ZnuC (NCBI) 161, 331
RSP_3569 zur Zinc-uptake regulator, Zur (NCBI) 161, 331
RSP_3571 znuA ABC zinc transporter, periplasmic binding protein ZnuA (NCBI) 161, 331
RSP_3664 RSP_3664 transcriptional regulator, GntR family (NCBI) 268, 331
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_3664
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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