Organism : Geobacter sulfurreducens | Module List :
GSU1345

RrF2 family protein (VIMSS)

CircVis
Functional Annotations (2)
Function System
Predicted transcriptional regulator cog/ cog
rrf2_super tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1345
(Mouseover regulator name to see its description)

GSU1345 is regulated by 13 influences and regulates 10 modules.
Regulators for GSU1345 (13)
Regulator Module Operator
GSU0534 290 tf
GSU1345 290 tf
GSU2185 290 tf
GSU2571 290 tf
GSU2945 290 tf
GSU3206 290 tf
GSU0041 201 tf
GSU0178 201 tf
GSU1495 201 tf
GSU1617 201 tf
GSU2041 201 tf
GSU2771 201 tf
GSU3370 201 tf

Warning: GSU1345 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
2562 2.30e+02 GCGgcAaCggc
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2563 1.60e+04 AtAtacAaTa.ATACtaatTAaC
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2738 4.00e+03 GgAAGGgA
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2739 9.70e+03 tTTgtTtTcTa
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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 GSU1345

GSU1345 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted transcriptional regulator cog/ cog
rrf2_super tigr/ tigrfam
Module neighborhood information for GSU1345

GSU1345 has total of 48 gene neighbors in modules 201, 290
Gene neighbors (48)
Gene Common Name Description Module membership
GSU0127 GSU0127 conserved hypothetical protein (VIMSS) 198, 201
GSU0192 GSU0192 hypothetical protein (VIMSS) 127, 290
GSU0304 pepN aminopeptidase N (NCBI) 53, 290
GSU0496 GSU0496 efflux transporter, RND family, MFP subunit (NCBI) 20, 290
GSU0534 GSU0534 RrF2 family protein (VIMSS) 262, 290
GSU0535 cysK cysteine synthase A (NCBI) 290, 321
GSU0536 GSU0536 conserved hypothetical protein TIGR00268 (VIMSS) 290, 318
GSU0537 GSU0537 sensory box/GGDEF family protein (VIMSS) 236, 290
GSU0623 GSU0623 glycosyl transferase, group 2 family protein (VIMSS) 131, 201
GSU0632 GSU0632 conserved hypothetical protein (VIMSS) 201, 329
GSU0769 rarD rarD protein (NCBI) 201, 318
GSU1183 mdeA O-acetyl-L-homoserine sulfhydrylase (NCBI) 223, 290
GSU1196 GSU1196 hypothetical protein (VIMSS) 125, 201
GSU1345 GSU1345 RrF2 family protein (VIMSS) 201, 290
GSU1378 pbpE beta-lactamase (NCBI) 69, 201
GSU1380 feoB-1 ferrous iron transport protein B (NCBI) 201, 318
GSU1382 GSU1382 iron-dependent repressor, putative (VIMSS) 201, 318
GSU1403 rluB ribosomal large subunit pseudouridine synthase B (NCBI) 46, 201
GSU1549 GSU1549 lipoprotein, putative (VIMSS) 84, 201
GSU1705 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase (NCBI) 88, 290
GSU1707 GSU1707 group II decarboxylase (VIMSS) 125, 290
GSU1708 GSU1708 chlorohydrolase, Atz/Trz family (VIMSS) 125, 290
GSU1709 smpB SsrA-binding protein (NCBI) 125, 290
GSU1762 GSU1762 TPR domain protein (VIMSS) 32, 201
GSU1763 GSU1763 DnaJ domain protein (VIMSS) 201, 291
GSU2011 GSU2011 cysteine desulfurase (VIMSS) 137, 290
GSU2012 GSU2012 NifU family protein (NCBI) 290, 318
GSU2024 GSU2024 hypothetical protein (VIMSS) 201, 221
GSU2048 GSU2048 hypothetical protein (NCBI) 201, 218
GSU2066 glgP glycogen phosphorylase (NCBI) 88, 201
GSU2194 guaA GMP synthase (NCBI) 51, 201
GSU2221 exeA general secretion pathway protein-related protein (NCBI) 201, 291
GSU2224 GSU2224 response regulator (VIMSS) 51, 201
GSU2240 galE UDP-glucose 4-epimerase (NCBI) 131, 201
GSU2301 GSU2301 hypothetical protein (VIMSS) 201, 203
GSU2568 GSU2568 MiaB-like tRNA modifying enzyme (NCBI) 172, 290
GSU2569 trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (NCBI) 172, 290
GSU2570 spl1 cysteine desulfurase (NCBI) 172, 290
GSU2571 GSU2571 RrF2 family protein (VIMSS) 172, 290
GSU2572 cysE serine acetyltransferase (NCBI) 172, 290
GSU2605 cmk cytidylate kinase (NCBI) 76, 201
GSU2946 tcrA DNA-binding heavy metal response regulator (NCBI) 76, 201
GSU3081 GSU3081 conserved hypothetical protein, truncation (NCBI) 174, 201
GSU3111 GSU3111 hypothetical protein (VIMSS) 290, 321
GSU3146 moaA molybdenum cofactor biosynthesis protein A, putative (NCBI) 201, 318
GSU3147 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB (NCBI) 164, 201
GSU3376 pleD GGDEF/response regulator receiver domain protein (NCBI) 201, 221
GSU3451 GSU3451 conserved hypothetical protein (VIMSS) 71, 201
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 GSU1345
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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