Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3436

transcriptional regulator, LysR-family (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3436
(Mouseover regulator name to see its description)

RSP_3436 is regulated by 14 influences and regulates 7 modules.
Regulators for RSP_3436 (14)
Regulator Module Operator
RSP_0386 186 tf
RSP_1032 186 tf
RSP_1486 186 tf
RSP_2800 186 tf
RSP_3238 186 tf
RSP_3341 186 tf
RSP_0386 111 tf
RSP_1014 111 tf
RSP_1032 111 tf
RSP_1776 111 tf
RSP_1790 111 tf
RSP_1871 111 tf
RSP_3436 111 tf
RSP_3464 111 tf

Warning: RSP_3436 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
7942 1.50e-13 tttTT.gatTtt..gAAtATAa.a
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7943 9.30e-03 AtGgtCtgcGccG..tGAa.cGA
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8092 1.40e-13 ttcCta.t.tctc.aacAACaAta
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8093 3.50e-05 TGGTCTaaacCGGtTcAGGaaaAA
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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_3436

RSP_3436 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for RSP_3436

RSP_3436 has total of 34 gene neighbors in modules 111, 186
Gene neighbors (34)
Gene Common Name Description Module membership
RSP_0460 RSP_0460 AcrB/AcrD/AcrF family cation/multidrug efflux pump (NCBI) 111, 185
RSP_0461 RSP_0461 multidrug/cation efflux pump, membrane fusion protein (MFP) family (NCBI) 111, 185
RSP_0462 RSP_0462 hypothetical protein (NCBI) 111, 236
RSP_1789 RSP_1789 hypothetical protein (NCBI) 89, 186
RSP_1790 RSP_1790 probable transcriptional regulator (NCBI) 89, 186
RSP_1791 RSP_1791 Heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase (NCBI) 89, 186
RSP_1825 tldD probable modulator of DNA gyrase (NCBI) 161, 186
RSP_1826 coxII Cytochrome c oxidase polypeptide II precursor (Cytochrome AA3 subunit 2) (NCBI) 131, 186
RSP_1827 cox10 Heme O synthase (NCBI) 131, 186
RSP_1828 cox11 cytochrome C oxidase assembly protein (NCBI) 131, 186
RSP_1829 coxIII Cytochrome c oxidase, aa3-type, subunit III (NCBI) 131, 186
RSP_2273 RSP_2273 putative anaerobic phenylacetate CoA ligase (NCBI) 135, 186
RSP_2274 RSP_2274 ABC branched amino acid transporter family, ATPase subunit (NCBI) 135, 186
RSP_2275 RSP_2275 ABC branched amino acid transporter family, periplasmic substrate-binding subunit (NCBI) 135, 186
RSP_2276 RSP_2276 ABC branched amino acid transporter family, inner membrane subunit (NCBI) 135, 186
RSP_2277 RSP_2277 ABC branched amino acid transporter family, inner membrane subunit (NCBI) 135, 186
RSP_2278 RSP_2278 ABC branched amino acid transporter family, ATPase subunit (NCBI) 135, 186
RSP_2279 RSP_2279 Long chain acyl-CoA synthetase (NCBI) 186, 347
RSP_3436 RSP_3436 transcriptional regulator, LysR-family (NCBI) 111, 186
RSP_3437 RSP_3437 Putative amino acid aminotransferase (NCBI) 111, 186
RSP_3438 RSP_3438 Translation initiation inhibitor (NCBI) 111, 186
RSP_3439 RSP_3439 Aspartate aminotransferase (NCBI) 111, 186
RSP_3440 RSP_3440 Putative short chain dehydrogenase (NCBI) 111, 186
RSP_3441 RSP_3441 hypothetical protein (NCBI) 111, 186
RSP_3442 RSP_3442 2-hydroxyacid dehydrogenase (NCBI) 111, 186
RSP_3457 RSP_3457 ABC polar amino acid transporter, periplasmic binding protein (NCBI) 111, 143
RSP_3458 RSP_3458 ABC polar amino acid transporter, ATPase subunit (NCBI) 111, 143
RSP_3459 RSP_3459 ABC polar amino acid transporter, inner membrane subunit (NCBI) 111, 143
RSP_3460 RSP_3460 ABC polar amino acid transporter, inner membrane subunit (NCBI) 111, 143
RSP_3461 RSP_3461 N-carbamyl-D-amino acid amidohydrolase (NCBI) 111, 143
RSP_3462 RSP_3462 putative D-hydantoinase dihydropyrimidinase (NCBI) 111, 143
RSP_3463 RSP_3463 putative hydantoin racemase (NCBI) 111, 143
RSP_3464 RSP_3464 transcriptional regulator, LysR-family (NCBI) 111, 143
RSP_3465 RSP_3465 hypothetical protein (NCBI) 111, 143
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_3436
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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