Organism : Geobacter sulfurreducens | Module List :
GSU3205

MiaB-like tRNA modifying enzyme YliG (NCBI)

CircVis
Functional Annotations (5)
Function System
2-methylthioadenine synthetase cog/ cog
metabolic process go/ biological_process
2-alkenal reductase [NAD(P)] activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
TIGR00089 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3205
(Mouseover regulator name to see its description)

GSU3205 is regulated by 26 influences and regulates 0 modules.
Regulators for GSU3205 (26)
Regulator Module Operator
GSU0063 47 tf
GSU0191 47 tf
GSU0205 47 tf
GSU0359 47 tf
GSU0812 47 tf
GSU2041 47 tf
GSU2523 47 tf
GSU2571 47 tf
GSU2581 47 tf
GSU3363 47 tf
GSU3370 47 tf
GSU3421 47 tf
GSU0013 147 tf
GSU0107 147 tf
GSU0254 147 tf
GSU0655 147 tf
GSU1013 147 tf
GSU1268 147 tf
GSU1345 147 tf
GSU1626 147 tf
GSU1887 147 tf
GSU2362 147 tf
GSU2523 147 tf
GSU3108 147 tf
GSU3363 147 tf
GSU3387 147 tf

Warning: GSU3205 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
2254 1.00e+04 CgcgTcCGCcg
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2255 2.10e+04 aAcatgtTCaAAaaA
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2454 1.10e+03 AtAAaaaCCTT.ACAAACggT
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2455 2.00e+04 acCacgAgcccGGaGGaAataCcg
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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 GSU3205

GSU3205 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
2-methylthioadenine synthetase cog/ cog
metabolic process go/ biological_process
2-alkenal reductase [NAD(P)] activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
TIGR00089 tigr/ tigrfam
Module neighborhood information for GSU3205

GSU3205 has total of 54 gene neighbors in modules 47, 147
Gene neighbors (54)
Gene Common Name Description Module membership
GSU0007 GSU0007 sensory box histidine kinase (VIMSS) 147, 159
GSU0107 spo0J parB-like domain protein (NCBI) 147, 181
GSU0259 GSU0259 flavoredoxin (VIMSS) 47, 222
GSU0446 GSU0446 conserved hypothetical protein TIGR00046 (VIMSS) 147, 183
GSU0524 GSU0524 conserved hypothetical protein (VIMSS) 47, 164
GSU0566 GSU0566 glutaredoxin family protein (NCBI) 47, 253
GSU0568 GSU0568 hypothetical protein (VIMSS) 47, 260
GSU0570 GSU0570 conserved hypothetical protein (VIMSS) 47, 70
GSU0572 GSU0572 HAD-superfamily hydrolase, subfamily IA, variant 3 (NCBI) 47, 159
GSU0606 alr alanine racemase (NCBI) 147, 231
GSU0607 selD selenide, water dikinase, selenocysteine-containing (NCBI) 147, 231
GSU0679 GSU0679 tellurite resistance protein-related protein (VIMSS) 25, 147
GSU0689 GSU0689 protein export membrane protein, SecD/SecF family, putative (VIMSS) 147, 309
GSU0751 GSU0751 conserved hypothetical protein (VIMSS) 147, 183
GSU0808 pleD GGDEF domain protein (NCBI) 47, 338
GSU0932 uraA uracil permease (NCBI) 147, 164
GSU1048 GSU1048 SEC-C motif domain protein (VIMSS) 8, 47
GSU1197 GSU1197 RNA methyltransferase, TrmH family, group 2, putative (NCBI) 40, 47
GSU1227 GSU1227 ABC transporter, ATP-binding protein (VIMSS) 11, 147
GSU1228 GSU1228 cytochrome c family protein (VIMSS) 11, 147
GSU1291 GSU1291 response regulator (VIMSS) 147, 158
GSU1356 GSU1356 ISGsu7, transposase OrfB (VIMSS) 47, 335
GSU1523 surE stationary-phase survival protein SurE (NCBI) 47, 70
GSU1527 GSU1527 conserved hypothetical protein (VIMSS) 147, 183
GSU1541 GSU1541 conserved hypothetical protein (VIMSS) 13, 147
GSU1543 GSU1543 hypothetical protein (VIMSS) 147, 262
GSU1612 gpm phosphoglycerate mutase (NCBI) 47, 338
GSU1838 hrpB ATP-dependent helicase HrpB (NCBI) 147, 338
GSU1917 uppS undecaprenyl diphosphate synthase (NCBI) 147, 333
GSU1923 GSU1923 membrane protein, putative (VIMSS) 47, 338
GSU1924 GSU1924 IPT/TIG domain protein (VIMSS) 47, 159
GSU2078 rodA rod shape-determining protein RodA (NCBI) 147, 207
GSU2088 GSU2088 glycosyl transferase, group 2 family protein (VIMSS) 47, 338
GSU2213 GSU2213 GAF domain protein (VIMSS) 47, 112
GSU2239 GSU2239 conserved hypothetical protein TIGR00255 (VIMSS) 47, 164
GSU2332 GSU2332 hypothetical protein (VIMSS) 8, 47
GSU2334 GSU2334 hypothetical protein (VIMSS) 59, 147
GSU2337 GSU2337 glycosyl transferase, group 20 family protein (NCBI) 47, 164
GSU2382 trpG anthranilate synthase component II (NCBI) 47, 196
GSU2545 maf maf protein (NCBI) 42, 147
GSU2647 GSU2647 conserved hypothetical protein (VIMSS) 11, 147
GSU2677 GSU2677 membrane protein, putative (VIMSS) 47, 338
GSU2683 panE 2-dehydropantoate 2-reductase (VIMSS) 47, 164
GSU2694 GSU2694 hypothetical protein (VIMSS) 17, 147
GSU2727 GSU2727 hypothetical protein (VIMSS) 11, 147
GSU2756 GSU2756 hypothetical protein (VIMSS) 147, 176
GSU2783 GSU2783 HDIG domain protein (VIMSS) 147, 296
GSU2929 GSU2929 conserved hypothetical protein (NCBI) 47, 70
GSU3133 GSU3133 penicillin-binding protein, 1A family (VIMSS) 47, 164
GSU3205 GSU3205 MiaB-like tRNA modifying enzyme YliG (NCBI) 47, 147
GSU3307 hisS histidyl-tRNA synthetase, putative (NCBI) 147, 245
GSU3310 GSU3310 hypothetical protein (VIMSS) 8, 47
GSU3353 rluD RNA pseudouridine synthase family protein (NCBI) 147, 289
GSU3371 GSU3371 AP endonuclease, family 2 (NCBI) 47, 164
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 GSU3205
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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