Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3694

Putative transcription activator (NCBI)

CircVis
Functional Annotations (3)
Function System
Putative transcription activator cog/ cog
thiaminase activity go/ molecular_function
Thiamine metabolism kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3694
(Mouseover regulator name to see its description)

RSP_3694 is regulated by 16 influences and regulates 25 modules.
Regulators for RSP_3694 (16)
Regulator Module Operator
RSP_0768 94 tf
RSP_1077 94 tf
RSP_1231 94 tf
RSP_1518 94 tf
RSP_1867 94 tf
RSP_2922 94 tf
RSP_3464 94 tf
RSP_3694 94 tf
RSP_0386 233 tf
RSP_1518 233 tf
RSP_1790 233 tf
RSP_2130 233 tf
RSP_2425 233 tf
RSP_2867 233 tf
RSP_3464 233 tf
RSP_3694 233 tf

Warning: RSP_3694 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
7908 8.50e-09 TtCtC..ccat.A.GaCatGAccc
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7909 3.50e-04 tCgACCTctgGggcacCaccGtCg
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8184 2.10e-07 CtGCatCcGcgCA.CCaaA.G
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8185 4.50e-02 AcaGGCGGGGgAtGggAAGGGGT
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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_3694

RSP_3694 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Putative transcription activator cog/ cog
thiaminase activity go/ molecular_function
Thiamine metabolism kegg/ kegg pathway
Module neighborhood information for RSP_3694

RSP_3694 has total of 48 gene neighbors in modules 94, 233
Gene neighbors (48)
Gene Common Name Description Module membership
RSP_0115 RSP_0115 Class I triheme cytochrome c (NCBI) 94, 313
RSP_0512 RSP_0512 multisensor hybrid histidine kinase (NCBI) 94, 304
RSP_0566 RSP_0566 possible transporter, DMT superfamily (NCBI) 94, 357
RSP_0700 RSP_0700 probable glycosyltransferase (NCBI) 233, 326
RSP_0701 RSP_0701 ABC peptide transporter, fused ATPase domains (NCBI) 233, 326
RSP_1069 RSP_1069 hypothetical protein (NCBI) 233, 267
RSP_1143 RSP_1143 4Fe-4S ferredoxin, iron-sulfur cluster binding protein (NCBI) 94, 326
RSP_1392 thiP ABC thiamine transporter, inner membrane subunit (NCBI) 233, 234
RSP_1414 RSP_1414 hypothetical protein (NCBI) 54, 94
RSP_1432 RSP_1432 hypothetical protein (NCBI) 94, 157
RSP_1631 RSP_1631 hypothetical protein (NCBI) 94, 347
RSP_1632 RSP_1632 hypothetical protein (NCBI) 94, 347
RSP_1633 RSP_1633 hypothetical protein (NCBI) 94, 347
RSP_1638 RSP_1638 hypothetical protein (NCBI) 233, 236
RSP_1639 RSP_1639 hypothetical protein (NCBI) 233, 253
RSP_1640 RSP_1640 hypothetical protein (NCBI) 168, 233
RSP_1641 RSP_1641 hypothetical protein (NCBI) 233, 300
RSP_1644 RSP_1644 hypothetical protein (NCBI) 233, 300
RSP_1645 RSP_1645 putative phage-related protein (NCBI) 191, 233
RSP_1646 RSP_1646 possible transmembrane protein (NCBI) 233, 308
RSP_1694 RSP_1694 Probable short-chain dehydrogenase/reductase (NCBI) 233, 304
RSP_1782 RSP_1782 hypothetical membrane protein (NCBI) 233, 235
RSP_1783 RSP_1783 Predicted membrane protein (NCBI) 233, 235
RSP_1900 RSP_1900 hypothetical protein (NCBI) 91, 233
RSP_1919 RSP_1919 hypothetical protein (NCBI) 94, 106
RSP_1964 RSP_1964 hypothetical protein (NCBI) 94, 147
RSP_2054 RSP_2054 hypothetical protein (NCBI) 31, 94
RSP_2057 RSP_2057 hypothetical protein (NCBI) 94, 347
RSP_2280 RSP_2280 PAS sensor hybrid histidine kinase (NCBI) 94, 325
RSP_2281 RSP_2281 two-component trancriptional regulator, winged helix family (NCBI) 94, 265
RSP_2874 RSP_2874 Putative Beta-glucosidase A (NCBI) 229, 233
RSP_2884 glgX glycogen debranching enzyme (NCBI) 233, 340
RSP_3122 RSP_3122 putative Glutathione S-transferase (NCBI) 233, 249
RSP_3287 upgC ABC glycerol-3-phosphate transporter, ATPase subunit UpgC (NCBI) 115, 233
RSP_3288 ugpE ABC glycerol-3-phosphate transporter, inner membrane subunit UgpE (NCBI) 115, 233
RSP_3289 ugpA ABC glycerol-3-phosphate transporter, inner membrane subunit UgpA (NCBI) 115, 233
RSP_3290 ugpB ABC glycerol-3-phosphate transporter, periplasmic binding protein, UgpB (NCBI) 115, 233
RSP_3632 RSP_3632 hypothetical protein (NCBI) 31, 94
RSP_3651 RSP_3651 putative membrane protein (NCBI) 189, 233
RSP_3652 RSP_3652 Predicted phage phi-C31 gp36 major capsid-like protein (NCBI) 141, 233
RSP_3653 RSP_3653 hypothetical protein (NCBI) 141, 233
RSP_3692 RSP_3692 Carbohydrate kinase, PfkB/Ribokinase (NCBI) 94, 189
RSP_3693 RSP_3693 BtpA protein (NCBI) 94, 233
RSP_3694 RSP_3694 Putative transcription activator (NCBI) 94, 233
RSP_3765 RSP_3765 hypothetical protein (NCBI) 94, 347
RSP_3766 RSP_3766 hypothetical protein (NCBI) 94, 347
RSP_3779 RSP_3779 hypothetical protein (NCBI) 94, 146
RSP_3788 RSP_3788 hypothetical protein (NCBI) 77, 233
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_3694
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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