Organism : Geobacter sulfurreducens | Module List :
GSU0107 spo0J

parB-like domain protein (NCBI)

CircVis
Functional Annotations (5)
Function System
Predicted transcriptional regulators cog/ cog
DNA binding go/ molecular_function
plasmid partitioning go/ biological_process
sequence-specific DNA binding go/ molecular_function
parB_part tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0107
(Mouseover regulator name to see its description)

GSU0107 is regulated by 20 influences and regulates 2 modules.
Regulators for GSU0107 spo0J (20)
Regulator Module Operator
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
GSU0372 181 tf
GSU1039 181 tf
GSU1495 181 tf
GSU2177 181 tf
GSU2520 181 tf
GSU2523 181 tf

Warning: GSU0107 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
2454 1.10e+03 AtAAaaaCCTT.ACAAACggT
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2455 2.00e+04 acCacgAgcccGGaGGaAataCcg
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2522 5.90e-02 gcgTtctTaaAAg.agttta
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2523 2.70e+02 tTcTCTTTGacttAcataaaa
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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 GSU0107

GSU0107 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted transcriptional regulators cog/ cog
DNA binding go/ molecular_function
plasmid partitioning go/ biological_process
sequence-specific DNA binding go/ molecular_function
parB_part tigr/ tigrfam
Module neighborhood information for GSU0107

GSU0107 has total of 61 gene neighbors in modules 147, 181
Gene neighbors (61)
Gene Common Name Description Module membership
GSU0007 GSU0007 sensory box histidine kinase (VIMSS) 147, 159
GSU0105 GSU0105 cytochrome c family protein, putative (NCBI) 180, 181
GSU0107 spo0J parB-like domain protein (NCBI) 147, 181
GSU0422 fliN flagellar motor switch protein FliN (NCBI) 181, 234
GSU0446 GSU0446 conserved hypothetical protein TIGR00046 (VIMSS) 147, 183
GSU0515 GSU0515 universal stress protein family (VIMSS) 69, 181
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
GSU0758 GSU0758 membrane protein, putative (VIMSS) 181, 278
GSU0932 uraA uracil permease (NCBI) 147, 164
GSU1039 GSU1039 sigma-54 dependent DNA-binding response regulator (VIMSS) 181, 269
GSU1047 GSU1047 conserved hypothetical protein (VIMSS) 181, 253
GSU1114 GSU1114 TPR domain protein (VIMSS) 181, 267
GSU1181 GSU1181 hypothetical protein (VIMSS) 176, 181
GSU1216 cydC transport ATP-binding protein CydC (NCBI) 8, 181
GSU1222 GSU1222 histone deacetylase/AcuC/AphA family protein (VIMSS) 106, 181
GSU1227 GSU1227 ABC transporter, ATP-binding protein (VIMSS) 11, 147
GSU1228 GSU1228 cytochrome c family protein (VIMSS) 11, 147
GSU1240 GSU1240 hypothetical protein (VIMSS) 176, 181
GSU1281 nikO component of nickel ABC transport system (Dmitry Rodionov) 181, 278
GSU1291 GSU1291 response regulator (VIMSS) 147, 158
GSU1310 GSU1310 pyridine nucleotide-disulfide oxidoreductase (Regina ONeil) 181, 205
GSU1319 GSU1319 sensor histidine kinase (VIMSS) 106, 181
GSU1446 GSU1446 radical SAM domain protein (NCBI) 181, 207
GSU1527 GSU1527 conserved hypothetical protein (VIMSS) 147, 183
GSU1541 GSU1541 conserved hypothetical protein (VIMSS) 13, 147
GSU1543 GSU1543 hypothetical protein (VIMSS) 147, 262
GSU1545 GSU1545 transporter, LysE family (VIMSS) 181, 338
GSU1573 GSU1573 CAAX amino terminal protease family protein (NCBI) 181, 253
GSU1715 GSU1715 hypothetical protein (VIMSS) 51, 181
GSU1740 GSU1740 cytochrome c family protein, putative (VIMSS) 69, 181
GSU1838 hrpB ATP-dependent helicase HrpB (NCBI) 147, 338
GSU1917 uppS undecaprenyl diphosphate synthase (NCBI) 147, 333
GSU2078 rodA rod shape-determining protein RodA (NCBI) 147, 207
GSU2116 GSU2116 hypothetical protein (VIMSS) 181, 253
GSU2117 GSU2117 hypothetical protein (VIMSS) 181, 278
GSU2163 GSU2163 hypothetical protein (VIMSS) 181, 278
GSU2177 GSU2177 hypothetical protein (VIMSS) 113, 181
GSU2293 GSU2293 hypothetical protein (VIMSS) 181, 338
GSU2297 GSU2297 sensory box histidine kinase (VIMSS) 71, 181
GSU2312 GSU2312 sulfate transporter family protein (VIMSS) 130, 181
GSU2334 GSU2334 hypothetical protein (VIMSS) 59, 147
GSU2472 vapC virulence associated protein C (NCBI) 181, 193
GSU2474 GSU2474 hypothetical protein (VIMSS) 88, 181
GSU2540 GSU2540 transcriptional regulator, Cro/CI family (VIMSS) 181, 304
GSU2545 maf maf protein (NCBI) 42, 147
GSU2647 GSU2647 conserved hypothetical protein (VIMSS) 11, 147
GSU2664 GSU2664 outer membrane efflux protein (VIMSS) 181, 244
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
GSU2927 GSU2927 cytochrome c, putative (NCBI) 181, 327
GSU3184 GSU3184 hypothetical protein (VIMSS) 181, 300
GSU3205 GSU3205 MiaB-like tRNA modifying enzyme YliG (NCBI) 47, 147
GSU3307 hisS histidyl-tRNA synthetase, putative (NCBI) 147, 245
GSU3353 rluD RNA pseudouridine synthase family protein (NCBI) 147, 289
GSU3361 GSU3361 transglutaminase domain protein (NCBI) 180, 181
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 GSU0107
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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