Organism : Geobacter sulfurreducens | Module List :
GSU0556

ISGsu7, transposase OrfB (VIMSS)

CircVis
Functional Annotations (3)
Function System
Transposase and inactivated derivatives cog/ cog
DNA binding go/ molecular_function
DNA integration go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0556
(Mouseover regulator name to see its description)

GSU0556 is regulated by 16 influences and regulates 0 modules.
Regulators for GSU0556 (16)
Regulator Module Operator
GSU0581 123 tf
GSU1201 123 tf
GSU1270 123 tf
GSU1495 123 tf
GSU1831 123 tf
GSU1934 123 tf
GSU2964 123 tf
GSU0736 62 tf
GSU1115 62 tf
GSU1250 62 tf
GSU1320 62 tf
GSU1727 62 tf
GSU2524 62 tf
GSU2831 62 tf
GSU2915 62 tf
GSU3387 62 tf

Warning: GSU0556 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
2284 1.50e-02 ttTtTtgtCtTgaca
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2285 3.10e+01 AAattatTG.aataatgG
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2406 1.30e+01 GgcGgtAtaCT
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2407 8.00e+02 AatTatAtagttGcATgaaa
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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 GSU0556

GSU0556 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transposase and inactivated derivatives cog/ cog
DNA binding go/ molecular_function
DNA integration go/ biological_process
Module neighborhood information for GSU0556

GSU0556 has total of 32 gene neighbors in modules 62, 123
Gene neighbors (32)
Gene Common Name Description Module membership
GSU0099 GSU0099 MglA protein (VIMSS) 50, 62
GSU0158 lysA diaminopimelate decarboxylase (NCBI) 62, 197
GSU0167 GSU0167 conserved hypothetical protein, truncation (NCBI) 62, 140
GSU0334 atpB ATP synthase F0, A subunit (NCBI) 62, 136
GSU0336 GSU0336 hypothetical protein (VIMSS) 62, 170
GSU0383 GSU0383 peptidyl-prolyl cis-trans isomerase, FKBP-type (NCBI) 62, 197
GSU0555 GSU0555 ISGsu7, transposase OrfA (VIMSS) 62, 123
GSU0556 GSU0556 ISGsu7, transposase OrfB (VIMSS) 62, 123
GSU0643 rpsP ribosomal protein S16 (NCBI) 50, 62
GSU0644 GSU0644 KH domain protein (VIMSS) 62, 154
GSU0866 GSU0866 YGGT family protein (VIMSS) 62, 197
GSU0872 GSU0872 lipoprotein, putative (VIMSS) 62, 197
GSU1212 GSU1212 conserved hypothetical protein (VIMSS) 3, 123
GSU1213 GSU1213 conserved hypothetical protein (VIMSS) 123, 288
GSU1242 asp aspartate aminotransferase (NCBI) 62, 328
GSU1464 GSU1464 LysM domain protein (VIMSS) 62, 197
GSU1557 GSU1557 mechanosensitive ion channel family protein (NCBI) 123, 187
GSU1559 GSU1559 hypothetical protein (VIMSS) 123, 177
GSU1599 rpmF ribosomal protein L32 (NCBI) 62, 169
GSU1629 gap glyceraldehyde 3-phosphate dehydrogenase 1 (NCBI) 62, 238
GSU1669 GSU1669 hypothetical protein (VIMSS) 123, 177
GSU1670 GSU1670 lipoprotein, putative (VIMSS) 123, 193
GSU1675 GSU1675 hypothetical protein (VIMSS) 113, 123
GSU1728 GSU1728 conserved hypothetical protein (VIMSS) 123, 240
GSU1895 pyrG CTP synthase (NCBI) 62, 161
GSU1899 GSU1899 virulence factor Mce family protein (VIMSS) 62, 328
GSU2091 purC phosphoribosylaminoimidazole-succinocarboxamidesynthase (NCBI) 62, 197
GSU2292 ald alanine dehydrogenase (NCBI) 123, 240
GSU2583 GSU2583 isochorismatase family protein (NCBI) 123, 187
GSU2585 GSU2585 hypothetical protein (VIMSS) 123, 128
GSU2874 argC N-acetyl-gamma-glutamyl-phosphate reductase (NCBI) 123, 288
GSU3351 GSU3351 hypothetical protein (VIMSS) 123, 187
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 GSU0556
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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