Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2079

hypothetical protein (NCBI)

CircVis
Functional Annotations (2)
Function System
Predicted transcriptional regulators cog/ cog
DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2079
(Mouseover regulator name to see its description)

RSP_2079 is regulated by 14 influences and regulates 7 modules.
Regulators for RSP_2079 (14)
Regulator Module Operator
RSP_1077 380 tf
RSP_1660 380 tf
RSP_2867 380 tf
RSP_3042 380 tf
RSP_3464 380 tf
RSP_1231 29 tf
RSP_1660 29 tf
RSP_1936 29 tf
RSP_2079 29 tf
RSP_2932 29 tf
RSP_3001 29 tf
RSP_3124 29 tf
RSP_3418 29 tf
RSP_3676 29 tf

Warning: RSP_2079 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
7778 5.10e+00 TGccaAaacTgcaGATtaGAagca
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7779 8.80e+00 CTtaCCggAtGtcaAagaaGgCG
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8450 7.30e-01 AtaaCCTTCATGcaa.c.Tt
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8451 2.00e+02 CTAaGgAcTtcatC
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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_2079

RSP_2079 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted transcriptional regulators cog/ cog
DNA binding go/ molecular_function
Module neighborhood information for RSP_2079

RSP_2079 has total of 39 gene neighbors in modules 29, 380
Gene neighbors (39)
Gene Common Name Description Module membership
RSP_0135 RSP_0135 hypothetical protein (NCBI) 29, 133
RSP_0136 RSP_0136 putative integrase for prophage CP-933U (NCBI) 29, 140
RSP_0456 RSP_0456 hypothetical protein (NCBI) 62, 380
RSP_0604 RSP_0604 hypothetical protein (NCBI) 29, 249
RSP_0813 RSP_0813 Response regulator receiver protein (NCBI) 29, 157
RSP_0860 RSP_0860 hypothetical protein (NCBI) 245, 380
RSP_0877 RSP_0877 Putative transporter, RhaT family, DMT superfamily (NCBI) 29, 187
RSP_1293 RSP_1293 putative acyl-carrier protein (NCBI) 267, 380
RSP_1303 flgE putative flagellar hook protein (NCBI) 29, 246
RSP_1500 RSP_1500 possible anti-sigma regulatory kinase (NCBI) 29, 304
RSP_1502 RSP_1502 GAF domain protein (NCBI) 29, 174
RSP_1637 RSP_1637 hypothetical protein (NCBI) 313, 380
RSP_1660 RSP_1660 putative ParB-like nuclease (NCBI) 88, 380
RSP_1662 RSP_1662 Integrase/recombinase (NCBI) 236, 380
RSP_1853 TrkH2 potassium uptake transporter, transmembrane component, TrkH (NCBI) 29, 67
RSP_1996 RSP_1996 Putative Competence protein (NCBI) 62, 380
RSP_2025 RSP_2025 hypothetical protein (NCBI) 29, 288
RSP_2034 RSP_2034 possible CAAX amino terminal protease family (NCBI) 235, 380
RSP_2043 RSP_2043 hypothetical protein (NCBI) 235, 380
RSP_2079 RSP_2079 hypothetical protein (NCBI) 29, 380
RSP_2372 RSP_2372 aldehyde dehydrogenase (NAD-dependent) (NCBI) 135, 380
RSP_2381 RSP_2381 putative 3-methyladenine DNA glycosylase (NCBI) 29, 101
RSP_2476 RSP_2476 hypothetical protein (NCBI) 29, 110
RSP_2990 RSP_2990 hypothetical protein (NCBI) 235, 380
RSP_3015 RSP_3015 hypothetical protein (NCBI) 29, 183
RSP_3097 qoxA QoxA, Quinol oxidase subunit I (NCBI) 19, 380
RSP_3245 RSP_3245 Possible transporter, Major facilitator superfamily (MFS) (NCBI) 176, 380
RSP_3286 iolB Uncharacterized enzyme involved in inositol metabolism, IolB (NCBI) 246, 380
RSP_3417 RSP_3417 TonB dependent outer membrane ferrichrome-iron receptor (NCBI) 235, 380
RSP_3772 RSP_3772 hypothetical protein (NCBI) 247, 380
RSP_3773 RSP_3773 hypothetical protein (NCBI) 189, 380
RSP_3774 RSP_3774 hypothetical protein (NCBI) 304, 380
RSP_3775 RSP_3775 hypothetical protein (NCBI) 304, 380
RSP_3776 RSP_3776 hypothetical protein (NCBI) 183, 380
RSP_3777 RSP_3777 hypothetical protein (NCBI) 29, 356
RSP_3783 RSP_3783 putative bacteriophage-related protein, Phage portal protein, lambda family (NCBI) 29, 183
RSP_3794 RSP_3794 hypothetical protein (NCBI) 29, 141
RSP_3798 RSP_3798 hypothetical protein (NCBI) 288, 380
RSP_3799 RSP_3799 hypothetical protein (NCBI) 288, 380
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_2079
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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