Organism : Geobacter sulfurreducens | Module List :
GSU0567 tag

DNA-3-methyladenine glycosylase I (NCBI)

CircVis
Functional Annotations (5)
Function System
3-methyladenine DNA glycosylase cog/ cog
base-excision repair go/ biological_process
DNA-3-methyladenine glycosylase I activity go/ molecular_function
Base excision repair kegg/ kegg pathway
tag tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0567
(Mouseover regulator name to see its description)

GSU0567 is regulated by 18 influences and regulates 0 modules.
Regulators for GSU0567 tag (18)
Regulator Module Operator
GSU0031 329 tf
GSU0041 329 tf
GSU0187 329 tf
GSU0280 329 tf
GSU1218 329 tf
GSU1495 329 tf
GSU2753 329 tf
GSU3045 329 tf
GSU0147 232 tf
GSU0721 232 tf
GSU0770 232 tf
GSU1382 232 tf
GSU1569 232 tf
GSU1831 232 tf
GSU2033 232 tf
GSU2041 232 tf
GSU2915 232 tf
GSU3324 232 tf

Warning: GSU0567 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
2624 2.30e+01 AaaggtaAAGatgtt.ttctG
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2625 1.70e+02 TTTTtccttgA
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2814 7.70e+04 TTTTTcAGT
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2815 3.10e+01 tTTtcaCgGaaAAg
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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 GSU0567

GSU0567 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
3-methyladenine DNA glycosylase cog/ cog
base-excision repair go/ biological_process
DNA-3-methyladenine glycosylase I activity go/ molecular_function
Base excision repair kegg/ kegg pathway
tag tigr/ tigrfam
Module neighborhood information for GSU0567

GSU0567 has total of 35 gene neighbors in modules 232, 329
Gene neighbors (35)
Gene Common Name Description Module membership
GSU0045 GSU0045 hypothetical protein (VIMSS) 232, 300
GSU0447 prmA ribosomal protein L11 methyltransferase (NCBI) 232, 282
GSU0567 tag DNA-3-methyladenine glycosylase I (NCBI) 232, 329
GSU0622 GSU0622 membrane protein, putative (NCBI) 76, 232
GSU0631 GSU0631 glycosyl transferase, group 2 family protein (VIMSS) 68, 329
GSU0632 GSU0632 conserved hypothetical protein (VIMSS) 201, 329
GSU0637 GSU0637 conserved hypothetical protein (VIMSS) 68, 329
GSU0747 GSU0747 conserved hypothetical protein (VIMSS) 104, 232
GSU0805 fsxA cytoplasmic membrane protein FsxA (NCBI) 232, 266
GSU0867 ubiE ubiquinone/menaquinone biosynthesis methyltransferase UbiE, putative (NCBI) 30, 329
GSU0913 GSU0913 ABC transporter, ATP-binding protein (VIMSS) 104, 232
GSU1179 GSU1179 hypothetical protein (NCBI) 29, 329
GSU1257 GSU1257 ABC transporter, periplasmic-substrate binding protein, putative (VIMSS) 104, 232
GSU1275 GSU1275 conserved hypothetical protein (VIMSS) 148, 329
GSU1359 GSU1359 helicase, putative (NCBI) 232, 293
GSU1423 pkcI HIT family protein (NCBI) 179, 232
GSU1462 GSU1462 RNA methyltransferase, TrmH family, group 3 (VIMSS) 204, 329
GSU1485 vacB ribonuclease R, putative (NCBI) 222, 329
GSU1566 GSU1566 hypothetical protein (VIMSS) 213, 232
GSU1700 maeB NADP-dependent malic enzyme (NCBI) 204, 329
GSU1701 GSU1701 HIT family protein (VIMSS) 204, 329
GSU1704 GSU1704 methyl-accepting chemotaxis protein, putative (VIMSS) 156, 329
GSU1768 GSU1768 ParA family protein (VIMSS) 176, 329
GSU1778 GSU1778 type II secretion system protein, putative (VIMSS) 316, 329
GSU1849 GSU1849 hypothetical protein (VIMSS) 87, 232
GSU1897 GSU1897 MTA/SAH nucleosidase, putative (VIMSS) 232, 329
GSU1958 GSU1958 polysaccharide deacetylase domain protein (NCBI) 213, 232
GSU2183 GSU2183 fic family protein (NCBI) 179, 232
GSU2252 GSU2252 heptosyltransferase family protein (VIMSS) 232, 324
GSU2399 GSU2399 conserved hypothetical protein (VIMSS) 179, 232
GSU2590 GSU2590 hypothetical protein (VIMSS) 232, 318
GSU2774 GSU2774 hypothetical protein (VIMSS) 180, 232
GSU3110 GSU3110 hypothetical protein (VIMSS) 262, 329
GSU3362 GSU3362 hypothetical protein (VIMSS) 232, 293
GSU3397 GSU3397 hypothetical protein (VIMSS) 232, 318
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 GSU0567
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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