Organism : Geobacter sulfurreducens | Module List :
GSU1693 hom

homoserine dehydrogenase (NCBI)

CircVis
Functional Annotations (10)
Function System
Homoserine dehydrogenase cog/ cog
homoserine dehydrogenase activity go/ molecular_function
cellular amino acid biosynthetic process go/ biological_process
amino acid binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Cysteine and methionine metabolism kegg/ kegg pathway
Lysine biosynthesis 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 GSU1693
(Mouseover regulator name to see its description)

GSU1693 is regulated by 19 influences and regulates 0 modules.
Regulators for GSU1693 hom (19)
Regulator Module Operator
GSU0732 263 tf
GSU1483 263 tf
GSU1525 263 tf
GSU1692 263 tf
GSU1727 263 tf
GSU2237 263 tf
GSU2581 263 tf
GSU2817 263 tf
GSU2831 263 tf
GSU3045 263 tf
GSU3087 263 tf
GSU0013 52 tf
GSU0031 52 tf
GSU1218 52 tf
GSU1483 52 tf
GSU1525 52 tf
GSU1692 52 tf
GSU1989 52 tf
GSU2149 52 tf

Warning: GSU1693 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
2264 2.00e+01 AattCaagtCgatacAcAATGcAa
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2265 1.20e+02 CgAtc.tCa.gc.GAatGGggC.G
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2686 3.30e+00 tcg.AaaAcccgtCaatTctaCca
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2687 4.00e+03 Tt.tTcCTTGAcgt
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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 GSU1693

GSU1693 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Homoserine dehydrogenase cog/ cog
homoserine dehydrogenase activity go/ molecular_function
cellular amino acid biosynthetic process go/ biological_process
amino acid binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Cysteine and methionine metabolism kegg/ kegg pathway
Lysine biosynthesis 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 GSU1693

GSU1693 has total of 33 gene neighbors in modules 52, 263
Gene neighbors (33)
Gene Common Name Description Module membership
GSU0162 aspC aromatic aminotransferase, putative (NCBI) 39, 263
GSU0327 hofF general secretion pathway protein F (NCBI) 28, 263
GSU0365 cyd-2 cytochrome c3 (NCBI) 52, 156
GSU0488 trxB thioredoxin reductase (NCBI) 80, 263
GSU0521 GSU0521 methyltransferase, putative (VIMSS) 5, 263
GSU0881 GSU0881 sensor histidine kinase (VIMSS) 52, 162
GSU1122 GSU1122 HD domain protein (NCBI) 52, 80
GSU1139 tyrS tyrosyl-tRNA synthetase (NCBI) 263, 316
GSU1150 GSU1150 oxidative cyclase-related protein (VIMSS) 80, 263
GSU1224 GSU1224 TPR domain protein (VIMSS) 255, 263
GSU1321 GSU1321 thioredoxin family protein (VIMSS) 52, 208
GSU1433 GSU1433 peptide ABC transporter, periplasmic peptide-binding protein (VIMSS) 52, 239
GSU1463 aspS aspartyl-tRNA synthetase (NCBI) 215, 263
GSU1530 hisG-1 ATP phosphoribosyltransferase (NCBI) 39, 52
GSU1692 nusB N utilization substance protein B (NCBI) 80, 263
GSU1693 hom homoserine dehydrogenase (NCBI) 52, 263
GSU1812 argS arginyl-tRNA synthetase (NCBI) 52, 332
GSU1827 nadB L-aspartate oxidase (NCBI) 80, 263
GSU1833 trpS tryptophanyl-tRNA synthetase (NCBI) 80, 263
GSU1880 metK S-adenosylmethionine synthetase (RefSeq) 137, 263
GSU1884 GSU1884 conserved hypothetical protein (VIMSS) 136, 263
GSU1885 hprK HPr(Ser) kinase/phosphatase (NCBI) 263, 313
GSU1894 kdsA 2-dehydro-3-deoxyphosphooctonate aldolase (NCBI) 5, 263
GSU2051 GSU2051 phenylacetate-coenzyme A ligase, putative (NCBI) 52, 227
GSU2052 GSU2052 indolepyruvate ferredoxin oxidoreductase, beta subunit, putative (VIMSS) 52, 227
GSU2053 GSU2053 indolepyruvate ferredoxin oxidoreductase, alpha subunit, putative (VIMSS) 52, 295
GSU2057 GSU2057 membrane protein, putative (VIMSS) 52, 227
GSU2105 GSU2105 hypothetical protein (VIMSS) 52, 239
GSU2270 GSU2270 ABC transporter, permease protein (VIMSS) 263, 277
GSU2271 lysS lysyl-tRNA synthetase (NCBI) 28, 263
GSU3073 GSU3073 None 52, 97
GSU3285 hemC porphobilinogen deaminase (NCBI) 44, 263
GSU3308 purA adenylosuccinate synthetase (NCBI) 52, 215
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 GSU1693
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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