Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0641

transcriptional regulator, XRE family (NCBI)

CircVis
Functional Annotations (3)
Function System
Predicted transcriptional regulators cog/ cog
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0641
(Mouseover regulator name to see its description)

RSP_0641 is regulated by 24 influences and regulates 12 modules.
Regulators for RSP_0641 (24)
Regulator Module Operator
RSP_1518 359 tf
RSP_1660 359 tf
RSP_2867 359 tf
RSP_3064 359 tf
RSP_3400 359 tf
RSP_3464 359 tf
RSP_3684 359 tf
RSP_3694 359 tf
RSP_0068 89 tf
RSP_0547 89 tf
RSP_0641 89 tf
RSP_0958 89 tf
RSP_1077 89 tf
RSP_1660 89 tf
RSP_1669 89 tf
RSP_1790 89 tf
RSP_2027 89 tf
RSP_2425 89 tf
RSP_2867 89 tf
RSP_3322 89 tf
RSP_3341 89 tf
RSP_3400 89 tf
RSP_3464 89 tf
RSP_3694 89 tf

Warning: RSP_0641 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
7898 1.70e-16 AAcaAttcAaaaacctaaaGTat
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7899 1.00e-06 aGtTTCCCGaTcgtG
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8416 3.00e-07 aAGaAaGGaaAAaccGaaAacAAA
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8417 8.10e-03 AaTcGCacTTaacCcTTGGcG
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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_0641

RSP_0641 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Predicted transcriptional regulators cog/ cog
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for RSP_0641

RSP_0641 has total of 30 gene neighbors in modules 89, 359
Gene neighbors (30)
Gene Common Name Description Module membership
RSP_0637 RSP_0637 hypothetical protein (NCBI) 89, 359
RSP_0638 RSP_0638 putative FAD dependent oxidoreductase protein (NCBI) 89, 359
RSP_0639 RSP_0639 Putative N-methylhydantoinase B (NCBI) 89, 359
RSP_0640 RSP_0640 putative N-methylhydantoinase A (NCBI) 89, 359
RSP_0641 RSP_0641 transcriptional regulator, XRE family (NCBI) 89, 359
RSP_0642 RSP_0642 possible transporter, RhaT family, DMT superfamily (NCBI) 89, 359
RSP_0986 RSP_0986 Panthothenate kinase (NCBI) 89, 122
RSP_0988 RSP_0988 ABC sugar transporter, ATPase subunit (NCBI) 89, 122
RSP_0989 RSP_0989 ABC sugar transporter, inner membrane subunit (NCBI) 89, 122
RSP_0990 RSP_0990 ABC sugar transporter, periplasmic sugar binding subunit (NCBI) 89, 122
RSP_0991 RSP_0991 Putative transcriptional regulator, ROK family (NCBI) 89, 122
RSP_1324 flgH Flagellar L-ring protein (NCBI) 153, 359
RSP_1325 RSP_1325 putative flagellar basal-body P-ring formation protein FlgA (NCBI) 153, 359
RSP_1326 RSP_1326 putative flagellar basal body rod protein (NCBI) 153, 359
RSP_1327 RSP_1327 putative flagellar basal body rod protein (NCBI) 153, 359
RSP_1328 RSP_1328 flagellar biosynthetic protein FliQ (NCBI) 153, 359
RSP_1329 fliE putative flagellar hook-basal body complex protein (NCBI) 153, 359
RSP_1330 RSP_1330 putative flagellar basal-body rod protein FlgC (NCBI) 153, 359
RSP_1331 RSP_1331 hypothetical protein (NCBI) 153, 359
RSP_1332 RSP_1332 H+-transporting two-sector ATPase, alpha/beta subunit (NCBI) 235, 359
RSP_1441 RSP_1441 regulatory protein, GntR family (NCBI) 89, 141
RSP_1442 RSP_1442 ABC sugar transporter, periplasmic sugar-binding protein (NCBI) 89, 106
RSP_1443 RSP_1443 ABC sugar transporter, inner membrane subunit (NCBI) 68, 89
RSP_1445 RSP_1445 ABC sugar transporter, ATPase subunit (NCBI) 68, 89
RSP_1446 RSP_1446 Putative sugar kinase (NCBI) 62, 89
RSP_1447 RSP_1447 possible glucosamine--fructose-6-phosphate aminotransferase (isomerizing) (NCBI) 89, 110
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_4313 RSP_4313 tRNA-Pro (NCBI) 179, 359
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_0641
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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