Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1741

Possible LuxR family protein (NCBI)

CircVis
Functional Annotations (6)
Function System
Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1741
(Mouseover regulator name to see its description)

RSP_1741 is regulated by 14 influences and regulates 21 modules.
Regulators for RSP_1741 (14)
Regulator Module Operator
RSP_0316 48 tf
RSP_0958 48 tf
RSP_1139 48 tf
RSP_1669 48 tf
RSP_2425 48 tf
RSP_2610 48 tf
RSP_3124 48 tf
RSP_3694 48 tf
RSP_0601 181 tf
RSP_1741 181 tf
RSP_1776 181 tf
RSP_2362 181 tf
RSP_2610 181 tf
RSP_2681 181 tf

Warning: RSP_1741 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
7816 1.20e-02 TTTtGaaTtt
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7817 5.60e-02 TTta.c.g.ttgAaAagacGa
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8082 6.20e+01 tatccgggg.cCAaAccgggAcg
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8083 4.40e-01 TTtTggGaAA
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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_1741

RSP_1741 is enriched for 6 functions in 3 categories.
Module neighborhood information for RSP_1741

RSP_1741 has total of 57 gene neighbors in modules 48, 181
Gene neighbors (57)
Gene Common Name Description Module membership
RSP_0002 spbB Histone-like nucleoid-structuring protein H-NS (NCBI) 48, 93
RSP_0019 RSP_0019 hypothetical protein (NCBI) 48, 285
RSP_0196 clpX ATP-dependent protease Clp, ATPase subunit (NCBI) 48, 52
RSP_0197 clpP Protease subunit of ATP-dependent Clp proteases (NCBI) 48, 345
RSP_0242 RSP_0242 probable kyurenine hydrolase (NCBI) 181, 294
RSP_0555 ruvA Holliday junction DNA helicase ruvA (NCBI) 4, 48
RSP_0556 ruvC Holliday junction nuclease RuvC (NCBI) 4, 48
RSP_0557 RSP_0557 hypothetical protein (NCBI) 3, 48
RSP_0717 RSP_0717 hypothetical protein (NCBI) 48, 81
RSP_0718 rpsU 30S ribosomal protein S21 (RpsU) (NCBI) 48, 56
RSP_0868 RSP_0868 putative transcriptional regulator (NCBI) 162, 181
RSP_1005 gshA putative glutathione synthetase (NCBI) 7, 181
RSP_1158 PtsN PTS IIA-like nitrogen-regulatory protein PtsN (NCBI) 149, 181
RSP_1383 RSP_1383 hypothetical protein (NCBI) 48, 277
RSP_1389 aroC Chorismate synthase (NCBI) 181, 234
RSP_1403 RSP_1403 conserved hypoothetical protein (NCBI) 58, 181
RSP_1496 RSP_1496 hypothetical protein (NCBI) 181, 327
RSP_1498 RSP_1498 hypothetical protein (NCBI) 181, 327
RSP_1517 spbA Histone-like protein of HNS family (NCBI) 48, 327
RSP_1624 RSP_1624 hypothetical protein (NCBI) 48, 208
RSP_1672 pdxJ PNP synthase, pyridoxal phosphate biosynthetic protein PdxJ (NCBI) 181, 286
RSP_1711 RSP_1711 Possible transporter, RhaT family, DMT superfamily (NCBI) 181, 302
RSP_1741 RSP_1741 Possible LuxR family protein (NCBI) 48, 181
RSP_1772 accA Acetyl-CoA carboxylase, alpha subunit (NCBI) 48, 182
RSP_1793 RSP_1793 Single-strand DNA binding protein (NCBI) 48, 261
RSP_1838 RSP_1838 hypothetical protein (NCBI) 63, 181
RSP_1864 RSP_1864 hypothetical protein (NCBI) 48, 309
RSP_1878 lipB Lipoate-protein ligase B (NCBI) 63, 181
RSP_1938 RSP_1938 Conserved hypotetical protein (NCBI) 181, 220
RSP_1985 RSP_1985 hypothetical protein (NCBI) 48, 368
RSP_2175 RSP_2175 ABC transporter, ATPase subunit (NCBI) 48, 341
RSP_2231 RSP_2231 hypothetical protein (NCBI) 181, 368
RSP_2245 hisH Glutamine amidotransferase (NCBI) 149, 181
RSP_2336 RSP_2336 hypothetical protein (NCBI) 71, 181
RSP_2379 RSP_2379 hypothetical protein (NCBI) 181, 368
RSP_2540 tatA twin-arginine translocation system protein, TatA (NCBI) 48, 237
RSP_2625 nifU NifU-related protein involved in Fe-S cluster formation (NCBI) 46, 48
RSP_2674 RSP_2674 hypothetical protein (NCBI) 48, 285
RSP_2681 rpoE sigma factor, RpoE (NCBI) 181, 368
RSP_2719 RSP_2719 transcriptional regulator, AsnC/Lrp family (NCBI) 181, 317
RSP_2763 RSP_2763 hypothetical protein (NCBI) 48, 64
RSP_2764 RSP_2764 hypothetical protein (NCBI) 48, 112
RSP_2773 RSP_2773 hypothetical protein (NCBI) 26, 48
RSP_2776 acpP Acyl carrier protein, AcpP (NCBI) 46, 48
RSP_2916 RSP_2916 hypothetical protein (NCBI) 124, 181
RSP_2945 cycJ cytochrome C-type biogenesis protein, CcmE (NCBI) 181, 218
RSP_2985 RSP_2985 hypothetical protein (NCBI) 71, 181
RSP_2987 RSP_2987 probable acetyltransferase (NCBI) 71, 181
RSP_3007 RSP_3007 hypothetical protein (NCBI) 48, 250
RSP_3127 arsC Putative arsenate reductase (NCBI) 54, 181
RSP_3548 RSP_3548 hypothetical protein (NCBI) 181, 271
RSP_3589 ihfB Integration host factor beta-subunit (NCBI) 48, 81
RSP_3634 RSP_3634 hypothetical protein (NCBI) 48, 379
RSP_4301 RSP_4301 tRNA-Leu (NCBI) 48, 327
RSP_4314 RSP_4314 tRNA-Ser (NCBI) 35, 48
RSP_4319 RSP_4319 tRNA-Gly (NCBI) 181, 220
RSP_4331 RSP_4331 tRNA-Pro (NCBI) 181, 225
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_1741
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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