Organism : Geobacter sulfurreducens | Module List :
GSU1607 glyA

Serine hydroxymethyltransferase (VIMSS)

CircVis
Functional Annotations (11)
Function System
Glycine/serine hydroxymethyltransferase cog/ cog
glycine hydroxymethyltransferase activity go/ molecular_function
glycine metabolic process go/ biological_process
L-serine metabolic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1607
(Mouseover regulator name to see its description)

GSU1607 is regulated by 18 influences and regulates 0 modules.
Regulators for GSU1607 glyA (18)
Regulator Module Operator
GSU0359 227 tf
GSU0366 227 tf
GSU1013 227 tf
GSU1483 227 tf
GSU1626 227 tf
GSU1934 227 tf
GSU2581 227 tf
GSU2666 227 tf
GSU3087 227 tf
GSU3229 227 tf
GSU0013 28 tf
GSU0366 28 tf
GSU1218 28 tf
GSU1687 28 tf
GSU1727 28 tf
GSU2149 28 tf
GSU2581 28 tf
GSU2666 28 tf

Warning: GSU1607 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
2216 5.90e+00 aGtcAAgaaaAAa
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2217 5.90e+02 attTtcaAgca.TTt
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2614 6.20e-01 agttttTTCAcattG
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2615 6.40e+00 tCgat.tTct.gacaAatgggGcA
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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 GSU1607

GSU1607 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Glycine/serine hydroxymethyltransferase cog/ cog
glycine hydroxymethyltransferase activity go/ molecular_function
glycine metabolic process go/ biological_process
L-serine metabolic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for GSU1607

GSU1607 has total of 31 gene neighbors in modules 28, 227
Gene neighbors (31)
Gene Common Name Description Module membership
GSU0320 GSU0320 hypothetical protein (VIMSS) 28, 332
GSU0325 GSU0325 general secretion pathway protein H, putative (NCBI) 28, 328
GSU0327 hofF general secretion pathway protein F (NCBI) 28, 263
GSU0329 GSU0329 general secretion pathway protein D, putative (VIMSS) 28, 245
GSU0489 GSU0489 Mg chelatase-related protein (VIMSS) 227, 239
GSU0579 glyS glycyl-tRNA synthetase, beta subunit (NCBI) 5, 227
GSU0580 ppdK pyruvate phosphate dikinase (NCBI) 5, 227
GSU1245 GSU1245 fructose-bisphosphate aldolase, class-II, putative (VIMSS) 28, 328
GSU1450 nth endonuclease III, putative (NCBI) 75, 227
GSU1604 acpP-2 acyl carrier protein (NCBI) 5, 227
GSU1607 glyA Serine hydroxymethyltransferase (VIMSS) 28, 227
GSU1798 GSU1798 2-isopropylmalate synthase/homocitrate synthase family protein (NCBI) 168, 227
GSU2051 GSU2051 phenylacetate-coenzyme A ligase, putative (NCBI) 52, 227
GSU2052 GSU2052 indolepyruvate ferredoxin oxidoreductase, beta subunit, putative (VIMSS) 52, 227
GSU2055 GSU2055 extracellular solute-binding protein, family 7 (VIMSS) 192, 227
GSU2056 GSU2056 tripartite ATP-independent periplasmic transporters, DctQ component, putative (NCBI) 227, 330
GSU2057 GSU2057 membrane protein, putative (VIMSS) 52, 227
GSU2255 GSU2255 conserved hypothetical protein (VIMSS) 28, 214
GSU2257 GSU2257 conserved hypothetical protein (VIMSS) 28, 277
GSU2258 lpxK tetraacyldisaccharide 4'-kinase (NCBI) 28, 277
GSU2259 GSU2259 3-deoxy-D-manno-octulosonic-acid transferase, putative (VIMSS) 28, 277
GSU2260 GSU2260 ABC transporter, ATP-binding protein, MsbA family (VIMSS) 28, 214
GSU2262 degT pleiotropic regulatory protein (NCBI) 28, 214
GSU2263 GSU2263 oxidoreductase, Gfo/Idh/MocA family (VIMSS) 3, 28
GSU2265 fabZ (3R)-hydroxymyristoyl-(acyl-carrier-protein) dehydratase (VIMSS) 28, 277
GSU2267 GSU2267 outer membrane protein, putative (VIMSS) 28, 277
GSU2271 lysS lysyl-tRNA synthetase (NCBI) 28, 263
GSU2291 GSU2291 phospho-2-dehydro-3-deoxyheptonate aldolase (VIMSS) 75, 227
GSU2556 GSU2556 peptidase, U32 family (VIMSS) 28, 328
GSU2609 pilB type IV pilus assembly protein, putative (NCBI) 227, 295
GSU3408 GSU3408 L-threonine aldolase, low-specificity (VIMSS) 3, 28
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 GSU1607
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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