Organism : Geobacter sulfurreducens | Module List :
GSU0860

methylenetetrahydrofolate reductase family protein (VIMSS)

CircVis
Functional Annotations (3)
Function System
5,10-methylenetetrahydrofolate reductase cog/ cog
methylenetetrahydrofolate reductase (NADPH) activity go/ molecular_function
methionine metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0860
(Mouseover regulator name to see its description)

GSU0860 is regulated by 17 influences and regulates 0 modules.
Regulators for GSU0860 (17)
Regulator Module Operator
GSU0514 126 tf
GSU0551 126 tf
GSU0770 126 tf
GSU1687 126 tf
GSU1692 126 tf
GSU1989 126 tf
GSU1992 126 tf
GSU2262 126 tf
GSU3421 126 tf
GSU0147 144 tf
GSU0205 144 tf
GSU0811 144 tf
GSU2041 144 tf
GSU2753 144 tf
GSU2952 144 tf
GSU3370 144 tf
GSU3421 144 tf

Warning: GSU0860 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
2412 8.80e+02 CtCctGgGGggcCGg
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2413 5.60e+03 TctCcaTtTtTcCCT
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2448 2.70e+04 taAgAaAAAA
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2449 6.90e+04 gggtCAAT.gaaaAaatcgcg
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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 GSU0860

GSU0860 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
5,10-methylenetetrahydrofolate reductase cog/ cog
methylenetetrahydrofolate reductase (NADPH) activity go/ molecular_function
methionine metabolic process go/ biological_process
Module neighborhood information for GSU0860

GSU0860 has total of 51 gene neighbors in modules 126, 144
Gene neighbors (51)
Gene Common Name Description Module membership
GSU0087 GSU0087 heterodisulfide reductase, iron-sulfur binding subunit, putative (VIMSS) 126, 214
GSU0089 GSU0089 heterodisulfide reductase subunit (VIMSS) 126, 291
GSU0090 GSU0090 heterodisulfide reductase subunit (VIMSS) 126, 214
GSU0091 GSU0091 heterodisulfide reductase subunit (VIMSS) 126, 214
GSU0213 GSU0213 radical SAM domain protein (NCBI) 126, 323
GSU0226 GSU0226 L-lactate permease, putative (VIMSS) 126, 164
GSU0271 glmU UDP-N-acetylglucosamine pyrophosphorylase (NCBI) 144, 336
GSU0370 GSU0370 hypothetical protein (VIMSS) 144, 156
GSU0487 GSU0487 cation efflux family protein (VIMSS) 144, 265
GSU0526 GSU0526 conserved hypothetical protein (VIMSS) 126, 281
GSU0825 GSU0825 pirin family protein (VIMSS) 126, 183
GSU0860 GSU0860 methylenetetrahydrofolate reductase family protein (VIMSS) 126, 144
GSU0861 GSU0861 conserved hypothetical protein (NCBI) 113, 144
GSU0862 folD-2 folD bifunctional protein (NCBI) 46, 126
GSU0887 GSU0887 conserved hypothetical protein (VIMSS) 144, 335
GSU0903 GSU0903 None 126, 317
GSU0925 GSU0925 ABC transporter, ATP-binding protein (VIMSS) 144, 163
GSU0949 GSU0949 efflux transporter, RND family, MFP subunit (NCBI) 144, 283
GSU1053 GSU1053 sensory box protein (VIMSS) 122, 126
GSU1124 coaBC phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase (NCBI) 126, 295
GSU1127 GSU1127 hypothetical protein (VIMSS) 144, 334
GSU1128 GSU1128 conserved hypothetical protein (VIMSS) 144, 334
GSU1180 ftsH-1 cell division protein FtsH (NCBI) 112, 126
GSU1202 rfbA mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase, truncation (NCBI) 51, 144
GSU1260 GSU1260 ABC transporter, permease protein (NCBI) 144, 204
GSU1274 GSU1274 radical SAM domain protein (NCBI) 126, 208
GSU1298 GSU1298 methyl-accepting chemotaxis protein (VIMSS) 126, 183
GSU1377 GSU1377 3-hydroxybutyryl-CoA dehydratase (VIMSS) 11, 126
GSU1461 pyrF orotidine 5`-phosphate decarboxylase (NCBI) 126, 233
GSU1535 recD exodeoxyribonuclease V, alpha subunit (NCBI) 126, 336
GSU1536 GSU1536 hypothetical protein (VIMSS) 144, 334
GSU1576 GSU1576 oxidoreductase, short chain dehydrogenase/reductase family (VIMSS) 144, 163
GSU1710 GSU1710 None 126, 249
GSU1808 folP dihydropteroate synthase (NCBI) 19, 144
GSU2047 GSU2047 conserved hypothetical protein (VIMSS) 26, 126
GSU2050 secA preprotein translocase, SecA subunit (NCBI) 91, 126
GSU2102 GSU2102 pyruvate formate-lyase-activating enzyme, putative (VIMSS) 126, 183
GSU2214 cheB-3 protein-glutamate methylesterase (NCBI) 126, 295
GSU2222 cheA-2 chemotaxis protein CheA (NCBI) 126, 222
GSU2272 GSU2272 lipoprotein, putative (VIMSS) 80, 126
GSU2342 GSU2342 membrane protein, putative (NCBI) 144, 163
GSU2375 GSU2375 None 126, 322
GSU2454 GSU2454 membrane protein, putative (VIMSS) 59, 144
GSU2567 GSU2567 sensor histidine kinase (VIMSS) 112, 144
GSU2673 GSU2673 hypothetical protein (VIMSS) 144, 296
GSU2717 GSU2717 conserved hypothetical protein (VIMSS) 144, 335
GSU2879 leuB 3-isopropylmalate dehydrogenase (NCBI) 126, 233
GSU3062 GSU3062 radical SAM domain protein (NCBI) 42, 126
GSU3260 GSU3260 phosphoserine aminotransferase, putative (VIMSS) 35, 126
GSU3421 GSU3421 transcriptional regulator, Crp/Fnr family (VIMSS) 126, 164
GSU3429 nuoN-2 NADH dehydrogenase I, N subunit (NCBI) 144, 336
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 GSU0860
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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