Organism : Geobacter sulfurreducens | Module List :
GSU1173 ogt

methylated-DNA--protein-cysteine methyltransferase, putative (NCBI)

CircVis
Functional Annotations (4)
Function System
Methylated DNA-protein cysteine methyltransferase cog/ cog
methylated-DNA-[protein]-cysteine S-methyltransferase activity go/ molecular_function
DNA repair go/ biological_process
ogt tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1173
(Mouseover regulator name to see its description)

GSU1173 is regulated by 17 influences and regulates 0 modules.
Regulators for GSU1173 ogt (17)
Regulator Module Operator
GSU0041 222 tf
GSU0164 222 tf
GSU0896 222 tf
GSU1495 222 tf
GSU1569 222 tf
GSU1992 222 tf
GSU2987 222 tf
GSU3370 222 tf
GSU0147 219 tf
GSU1320 219 tf
GSU1419 219 tf
GSU1495 219 tf
GSU1525 219 tf
GSU1934 219 tf
GSU2523 219 tf
GSU2945 219 tf
GSU3363 219 tf

Warning: GSU1173 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
2598 1.20e+02 tgtcgg.gtgcTGaAg..tg
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2599 5.80e+03 CgaTgAACaacGcAa
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2604 4.70e-01 cttaaaTtcT..CcGcAAgGggAC
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2605 3.30e+02 AAaaTGcaAagGgTTTTTcaGTGa
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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 GSU1173

GSU1173 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Methylated DNA-protein cysteine methyltransferase cog/ cog
methylated-DNA-[protein]-cysteine S-methyltransferase activity go/ molecular_function
DNA repair go/ biological_process
ogt tigr/ tigrfam
Module neighborhood information for GSU1173

GSU1173 has total of 38 gene neighbors in modules 219, 222
Gene neighbors (38)
Gene Common Name Description Module membership
GSU0156 argH argininosuccinate lyase (NCBI) 222, 289
GSU0157 GSU0157 fibronectin type III domain protein (NCBI) 71, 222
GSU0257 GSU0257 conserved hypothetical protein (VIMSS) 198, 222
GSU0258 GSU0258 hypothetical protein (VIMSS) 59, 222
GSU0259 GSU0259 flavoredoxin (VIMSS) 47, 222
GSU0461 fabG-1 3-oxoacyl-(acyl carrier protein) reductase (NCBI) 67, 222
GSU0513 GSU0513 dephospho-CoA kinase (VIMSS) 212, 219
GSU0565 GSU0565 hypothetical protein (VIMSS) 163, 222
GSU0742 GSU0742 NAD-dependent dehydrogenase subunit (VIMSS) 222, 265
GSU0796 GSU0796 acyl-CoA thioester hydrolase, putative (NCBI) 213, 222
GSU1011 GSU1011 hypothetical protein (VIMSS) 208, 219
GSU1137 GSU1137 KH domain/HD domain protein (NCBI) 207, 222
GSU1173 ogt methylated-DNA--protein-cysteine methyltransferase, putative (NCBI) 219, 222
GSU1282 GSU1282 hypothetical protein (VIMSS) 98, 219
GSU1313 GSU1313 carboxymuconolactone decarboxylase (VIMSS) 43, 219
GSU1419 GSU1419 transcriptional regulator, Cro/CI family (VIMSS) 219, 236
GSU1421 GSU1421 nuclease SbcCD, D subunit, putative (NCBI) 212, 219
GSU1422 GSU1422 nuclease SbcCD, C subunit, putative (NCBI) 212, 219
GSU1484 GSU1484 soluble lytic murein transglycosylase, putative (VIMSS) 204, 222
GSU1485 vacB ribonuclease R, putative (NCBI) 222, 329
GSU1488 GSU1488 membrane protein, putative (VIMSS) 75, 222
GSU1531 hisI phosphoribosyl-AMP cyclohydrolase (NCBI) 219, 255
GSU1578 mutA B12-binding protein (NCBI) 139, 219
GSU1579 GSU1579 LAO/AO transport system ATPase (VIMSS) 219, 231
GSU1580 GSU1580 ErfK/YbiS/YcfS/YnhG family protein (NCBI) 68, 219
GSU1668 GSU1668 hypothetical protein (VIMSS) 219, 324
GSU1730 livF branched-chain amino acid ABC transporter, ATP-binding protein (NCBI) 219, 255
GSU1839 GSU1839 hydrolase, haloacid dehalogenase-like family (VIMSS) 98, 219
GSU1840 GSU1840 PAP2 family protein (VIMSS) 8, 219
GSU1928 GSU1928 sensor histidine kinase/response regulator (VIMSS) 219, 324
GSU1991 GSU1991 CAAX amino terminal protease family protein (NCBI) 222, 278
GSU2026 aroK shikimate kinase (NCBI) 219, 221
GSU2027 aroC chorismate synthase (NCBI) 139, 219
GSU2125 GSU2125 conserved domain protein (VIMSS) 59, 222
GSU2222 cheA-2 chemotaxis protein CheA (NCBI) 126, 222
GSU2947 GSU2947 sensor histidine kinase (VIMSS) 67, 222
GSU2956 GSU2956 redox-active disulfide protein 2 (VIMSS) 43, 219
GSU3164 GSU3164 hypothetical protein (VIMSS) 222, 334
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 GSU1173
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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