Organism : Geobacter sulfurreducens | Module List :
GSU0227

type II DNA modification methyltransferase, putative (NCBI)

CircVis
Functional Annotations (8)
Function System
Site-specific DNA methylase cog/ cog
DNA binding go/ molecular_function
DNA methylation go/ biological_process
DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates go/ molecular_function
DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates go/ molecular_function
DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates go/ molecular_function
Cysteine and methionine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0227
(Mouseover regulator name to see its description)

GSU0227 is regulated by 17 influences and regulates 0 modules.
Regulators for GSU0227 (17)
Regulator Module Operator
GSU0191 253 tf
GSU2041 253 tf
GSU3298 253 tf
GSU3396 253 tf
GSU3421 253 tf
GSU0164 164 tf
GSU0267 164 tf
GSU0470 164 tf
GSU0598 164 tf
GSU0776 164 tf
GSU1687 164 tf
GSU1989 164 tf
GSU2041 164 tf
GSU2523 164 tf
GSU2809 164 tf
GSU3060 164 tf
GSU3421 164 tf

Warning: GSU0227 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
2488 8.60e-01 aTGaCTtGTatgAcAAAtTCG
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2489 9.90e-01 GCgCatCttcgCCgcCgaCgC
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2666 3.50e+02 tgAaaatg.tGCtGTgcatGa
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2667 1.30e+03 AAGGggAAtaa
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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 GSU0227

GSU0227 is enriched for 8 functions in 3 categories.
Module neighborhood information for GSU0227

GSU0227 has total of 50 gene neighbors in modules 164, 253
Gene neighbors (50)
Gene Common Name Description Module membership
GSU0226 GSU0226 L-lactate permease, putative (VIMSS) 126, 164
GSU0227 GSU0227 type II DNA modification methyltransferase, putative (NCBI) 164, 253
GSU0250 GSU0250 conserved hypothetical protein (VIMSS) 25, 253
GSU0279 GSU0279 cadherin domain/calx-beta domain protein (NCBI) 45, 253
GSU0289 GSU0289 conserved hypothetical protein (VIMSS) 8, 253
GSU0457 GSU0457 lipoprotein, putative (VIMSS) 125, 164
GSU0458 GSU0458 (3R)-hydroxymyristoyl-(acyl-carrier-protein) dehydratase, putative (VIMSS) 125, 164
GSU0474 GSU0474 sensory box/GGDEF family protein (VIMSS) 40, 253
GSU0524 GSU0524 conserved hypothetical protein (VIMSS) 47, 164
GSU0541 polA DNA polymerase I (NCBI) 164, 183
GSU0566 GSU0566 glutaredoxin family protein (NCBI) 47, 253
GSU0621 GSU0621 hypothetical protein (NCBI) 60, 253
GSU0841 GSU0841 sigma-54 dependent DNA-binding response regulator (VIMSS) 164, 281
GSU0853 GSU0853 CBS domain protein (VIMSS) 65, 253
GSU0854 GSU0854 membrane protein (NCBI) 65, 164
GSU0858 GSU0858 TonB-dependent receptor, putative (VIMSS) 9, 164
GSU0863 GSU0863 conserved hypothetical protein (VIMSS) 57, 253
GSU0932 uraA uracil permease (NCBI) 147, 164
GSU0934 GSU0934 hypothetical protein (VIMSS) 8, 164
GSU0970 GSU0970 conserved hypothetical protein (VIMSS) 153, 253
GSU0997 mutM formamidopyrimidine-DNA glycosylase (NCBI) 40, 164
GSU1009 hflX GTP-binding protein (NCBI) 164, 253
GSU1047 GSU1047 conserved hypothetical protein (VIMSS) 181, 253
GSU1190 GSU1190 conserved hypothetical protein (VIMSS) 46, 253
GSU1297 GSU1297 ISGsu2, transposase (VIMSS) 72, 164
GSU1548 GSU1548 hypothetical protein (VIMSS) 40, 253
GSU1562 GSU1562 conserved hypothetical protein TIGR00106 (VIMSS) 164, 253
GSU1563 GSU1563 hypothetical protein (VIMSS) 97, 164
GSU1573 GSU1573 CAAX amino terminal protease family protein (NCBI) 181, 253
GSU1770 GSU1770 hypothetical protein (VIMSS) 133, 253
GSU2082 GSU2082 conserved hypothetical protein (VIMSS) 253, 321
GSU2116 GSU2116 hypothetical protein (VIMSS) 181, 253
GSU2159 GSU2159 hypothetical protein (VIMSS) 6, 253
GSU2239 GSU2239 conserved hypothetical protein TIGR00255 (VIMSS) 47, 164
GSU2337 GSU2337 glycosyl transferase, group 20 family protein (NCBI) 47, 164
GSU2414 GSU2414 membrane protein, putative (VIMSS) 164, 183
GSU2674 GSU2674 hypothetical protein (VIMSS) 164, 323
GSU2683 panE 2-dehydropantoate 2-reductase (VIMSS) 47, 164
GSU2736 GSU2736 hypothetical protein (VIMSS) 164, 327
GSU2750 GSU2750 conserved domain protein (VIMSS) 57, 253
GSU2772 GSU2772 ISGsu3, transposase (VIMSS) 84, 253
GSU2930 GSU2930 cytochrome c family protein (VIMSS) 253, 321
GSU3049 GSU3049 hypothetical protein (VIMSS) 160, 164
GSU3118 regX3 DNA-binding response regulator (NCBI) 253, 278
GSU3133 GSU3133 penicillin-binding protein, 1A family (VIMSS) 47, 164
GSU3147 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB (NCBI) 164, 201
GSU3314 GSU3314 lipoprotein, putative (VIMSS) 164, 183
GSU3371 GSU3371 AP endonuclease, family 2 (NCBI) 47, 164
GSU3411 pcrA ATP-dependent DNA helicase PcrA, putative (NCBI) 164, 281
GSU3421 GSU3421 transcriptional regulator, Crp/Fnr family (VIMSS) 126, 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 GSU0227
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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