Organism : Geobacter sulfurreducens | Module List :
GSU2779

transcriptional regulator, MerR family (VIMSS)

CircVis
Functional Annotations (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2779
(Mouseover regulator name to see its description)

GSU2779 is regulated by 19 influences and regulates 13 modules.
Regulators for GSU2779 (19)
Regulator Module Operator
GSU0470 130 tf
GSU0811 130 tf
GSU1268 130 tf
GSU1342 130 tf
GSU2202 130 tf
GSU2716 130 tf
GSU2753 130 tf
GSU2779 130 tf
GSU3418 130 tf
GSU3421 130 tf
GSU0266 148 tf
GSU0473 148 tf
GSU1115 148 tf
GSU1320 148 tf
GSU1831 148 tf
GSU2779 148 tf
GSU2915 148 tf
GSU3217 148 tf
GSU3324 148 tf

Warning: GSU2779 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
2420 3.20e+01 tTaaatatttt.tca.aaTat
Loader icon
2421 6.40e+03 ttgCCgatAc..taaAaaaactcA
Loader icon
2456 1.40e+04 AA.aAaTT.Aa.Ta.AtTAA
Loader icon
2457 1.40e+04 TGC.GcgGttaaGC.GgCGtA
Loader icon
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 GSU2779

GSU2779 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for GSU2779

GSU2779 has total of 46 gene neighbors in modules 130, 148
Gene neighbors (46)
Gene Common Name Description Module membership
GSU0163 GSU0163 hypothetical protein (VIMSS) 148, 206
GSU0352 psaD thiol peroxidase (NCBI) 130, 315
GSU0431 GSU0431 conserved hypothetical protein (VIMSS) 96, 130
GSU0480 GSU0480 NifU-like domain protein (NCBI) 130, 178
GSU0502 GSU0502 lipoprotein, putative (VIMSS) 130, 322
GSU0608 GSU0608 conserved domain protein (NCBI) 130, 231
GSU0617 GSU0617 NHL repeat domain protein (VIMSS) 121, 148
GSU0699 GSU0699 HD domain protein (NCBI) 148, 283
GSU0763 GSU0763 helicase, putative (NCBI) 130, 180
GSU0842 GSU0842 sensory box histidine kinase/response regulator (VIMSS) 63, 148
GSU0892 GSU0892 None 78, 130
GSU0956 GSU0956 hypothetical protein (VIMSS) 105, 148
GSU1042 GSU1042 conserved hypothetical protein (NCBI) 130, 278
GSU1164 GSU1164 ABC transporter, permease protein (VIMSS) 130, 278
GSU1214 GSU1214 tetracenomycin polyketide synthesis 8-o-methyltransferase, putative (NCBI) 148, 180
GSU1232 GSU1232 hypothetical protein (VIMSS) 30, 148
GSU1268 GSU1268 transcriptional regulator, LysR family (VIMSS) 130, 190
GSU1275 GSU1275 conserved hypothetical protein (VIMSS) 148, 329
GSU1384 cas3 CRISPR-associated helicase Cas3 (NCBI) 94, 130
GSU1388 GSU1388 CRISPR-associated protein, CT1976 family (NCBI) 36, 130
GSU1581 GSU1581 polyA polymerase family protein (NCBI) 130, 180
GSU1878 GSU1878 sensor histidine kinase (VIMSS) 30, 148
GSU2309 GSU2309 metallo-beta-lactamase family protein (VIMSS) 96, 130
GSU2310 GSU2310 YeeE/YedE family protein (NCBI) 130, 269
GSU2311 GSU2311 YeeE/YedE family protein (NCBI) 115, 130
GSU2312 GSU2312 sulfate transporter family protein (VIMSS) 130, 181
GSU2331 GSU2331 conserved hypothetical protein (VIMSS) 118, 148
GSU2371 trpA tryptophan synthase, alpha subunit (NCBI) 88, 148
GSU2748 GSU2748 cytochrome c family protein, putative (NCBI) 103, 130
GSU2749 GSU2749 NOL1/NOP2/sun family protein (VIMSS) 130, 140
GSU2779 GSU2779 transcriptional regulator, MerR family (VIMSS) 130, 148
GSU2781 GSU2781 efflux transporter, RND family, MFP subunit (NCBI) 130, 296
GSU2890 GSU2890 cytochrome c biogenesis protein, CcmF/CcyK/CcsA family (VIMSS) 130, 300
GSU2892 GSU2892 hypothetical protein (VIMSS) 124, 130
GSU2893 GSU2893 hypothetical protein (VIMSS) 130, 140
GSU2950 GSU2950 ABC transporter, permease protein (VIMSS) 103, 130
GSU2951 GSU2951 ABC transporter, ATP-binding protein (VIMSS) 130, 146
GSU2981 GSU2981 TonB-dependent receptor, putative (VIMSS) 14, 148
GSU3162 GSU3162 L-allo-threonine aldolase (VIMSS) 148, 153
GSU3166 GSU3166 conserved hypothetical protein (VIMSS) 130, 322
GSU3167 GSU3167 hypothetical protein (VIMSS) 70, 130
GSU3168 GSU3168 beta-ketoacyl synthase domain protein (NCBI) 130, 337
GSU3179 GSU3179 conserved domain protein (NCBI) 105, 130
GSU3367 ispF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (NCBI) 84, 148
GSU3369 selA L-seryl-tRNA selenium transferase (NCBI) 148, 235
GSU3426 GSU3426 hypothetical protein (VIMSS) 148, 180
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 GSU2779
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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