Organism : Geobacter sulfurreducens | Module List :
GSU1515 thrS

threonyl-tRNA synthetase (NCBI)

CircVis
Functional Annotations (7)
Function System
Threonyl-tRNA synthetase cog/ cog
threonine-tRNA ligase activity go/ molecular_function
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
threonyl-tRNA aminoacylation go/ biological_process
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
thrS tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1515
(Mouseover regulator name to see its description)

GSU1515 is regulated by 14 influences and regulates 0 modules.
Regulators for GSU1515 thrS (14)
Regulator Module Operator
GSU0207 116 tf
GSU0284 116 tf
GSU0770 116 tf
GSU1569 116 tf
GSU1586 116 tf
GSU1905 116 tf
GSU2831 116 tf
GSU2915 116 tf
GSU0372 101 tf
GSU1270 101 tf
GSU1483 101 tf
GSU2237 101 tf
GSU2524 101 tf
GSU3087 101 tf

Warning: GSU1515 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
2362 4.20e-02 TaaAcAAA
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2363 3.40e+00 aAAgTGTaTaCagtAtgC
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2392 1.40e+02 ataAaatTGACtAAt
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2393 8.10e+02 AaAAGTAA
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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 GSU1515

GSU1515 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Threonyl-tRNA synthetase cog/ cog
threonine-tRNA ligase activity go/ molecular_function
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
threonyl-tRNA aminoacylation go/ biological_process
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
thrS tigr/ tigrfam
Module neighborhood information for GSU1515

GSU1515 has total of 41 gene neighbors in modules 101, 116
Gene neighbors (41)
Gene Common Name Description Module membership
GSU0037 serS seryl-tRNA synthetase (NCBI) 37, 116
GSU0159 dapA dihydrodipicolinate synthase (NCBI) 101, 214
GSU0207 GSU0207 cold-shock domain family protein (VIMSS) 18, 116
GSU0298 GSU0298 sigma-54 dependent DNA-binding response regulator, interruption-C (VIMSS) 116, 169
GSU0333 atpE ATP synthase F0, C subunit (NCBI) 116, 170
GSU0509 sfrA Fe(III) reductase, alpha subunit (NCBI) 101, 243
GSU0510 sfrB Fe(III) reductase, beta subunit (NCBI) 101, 243
GSU0592 GSU0592 cytochrome c family protein (NCBI) 18, 116
GSU0666 rpsR ribosomal protein S18 (NCBI) 26, 116
GSU0667 GSU0667 membrane protein, putative (VIMSS) 26, 116
GSU0864 GSU0864 conserved hypothetical protein TIGR00251 (VIMSS) 101, 214
GSU0994 fumB fumarate hydratase, class I (NCBI) 101, 243
GSU1106 GSU1106 citrate synthase (NCBI) 101, 243
GSU1126 GSU1126 phage SPO1 DNA polymerase-related protein (VIMSS) 101, 225
GSU1176 GSU1176 fumarate reductase, cytochrome b subunit, putative (VIMSS) 101, 228
GSU1177 frdA fumarate reductase, flavoprotein subunit (NCBI) 101, 214
GSU1465 icd isocitrate dehydrogenase, NADP-dependent (NCBI) 101, 297
GSU1466 mdh malate dehydrogenase (NCBI) 101, 297
GSU1515 thrS threonyl-tRNA synthetase (NCBI) 101, 116
GSU1518 rplT ribosomal protein L20 (NCBI) 56, 116
GSU1660 acnB aconitate hydratase 2 (NCBI) 101, 169
GSU1902 leuD 3-isopropylmalate dehydratase, small subunit, putative (NCBI) 101, 169
GSU1905 GSU1905 cold shock domain family protein (VIMSS) 56, 116
GSU2223 cheY-6 chemotaxis protein CheY (NCBI) 101, 238
GSU2427 GSU2427 hypothetical protein (VIMSS) 101, 225
GSU2707 ackA-1 acetate kinase (NCBI) 101, 168
GSU2708 GSU2708 ferredoxin family protein (VIMSS) 101, 228
GSU2830 rplQ ribosomal protein L17 (NCBI) 116, 340
GSU2833 rpsK ribosomal protein S11 (NCBI) 24, 116
GSU2837 secY preprotein translocase, SecY subunit (NCBI) 116, 333
GSU2860 fusA-3 translation elongation factor G (NCBI) 37, 116
GSU2867 rplK ribosomal protein L11 (NCBI) 58, 116
GSU2915 GSU2915 sigma-54 dependent DNA-binding response regulator (VIMSS) 11, 116
GSU3005 thiC-2 thiamine biosynthesis protein ThiC (NCBI) 101, 169
GSU3007 GSU3007 phosphoglycerate mutase family, putative (VIMSS) 101, 169
GSU3009 cobT nicotinate-nucleotide--dimethylbenzimidazolephosphoribosyltransferase (NCBI) 101, 169
GSU3011 GSU3011 hypothetical protein (VIMSS) 97, 101
GSU3132 huP-2 DNA-binding protein HU (NCBI) 35, 116
GSU3237 GSU3237 hypothetical protein (VIMSS) 116, 238
GSU3454 GSU3454 radical SAM domain protein (NCBI) 60, 116
GSU3467 GSU3467 conserved hypothetical protein TIGR00278 (VIMSS) 116, 267
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 GSU1515
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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