Organism : Geobacter sulfurreducens | Module List :
GSU1805 glmM

phosphoglucosamine mutase (NCBI)

CircVis
Functional Annotations (6)
Function System
Phosphomannomutase cog/ cog
carbohydrate metabolic process go/ biological_process
phosphoglucosamine mutase activity go/ molecular_function
Amino sugar and nucleotide sugar metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
glmM tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1805
(Mouseover regulator name to see its description)

GSU1805 is regulated by 23 influences and regulates 0 modules.
Regulators for GSU1805 glmM (23)
Regulator Module Operator
GSU0280 102 tf
GSU0581 102 tf
GSU1495 102 tf
GSU1522 102 tf
GSU1831 102 tf
GSU1934 102 tf
GSU2033 102 tf
GSU2523 102 tf
GSU2581 102 tf
GSU2753 102 tf
GSU0031 143 tf
GSU0041 143 tf
GSU0187 143 tf
GSU0581 143 tf
GSU0732 143 tf
GSU1218 143 tf
GSU1320 143 tf
GSU1495 143 tf
GSU1525 143 tf
GSU1692 143 tf
GSU2753 143 tf
GSU3041 143 tf
GSU3089 143 tf

Warning: GSU1805 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
2364 3.60e+02 AAAATTACCTGATTAGCACTAA
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2365 7.60e+00 GAggGGgaGatTccTGGtgGcTga
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2446 1.50e+01 tT.Tta.AtTttT
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2447 4.10e+03 aA.GacaAaaC.c..ctGg.gcgt
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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 GSU1805

GSU1805 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Phosphomannomutase cog/ cog
carbohydrate metabolic process go/ biological_process
phosphoglucosamine mutase activity go/ molecular_function
Amino sugar and nucleotide sugar metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
glmM tigr/ tigrfam
Module neighborhood information for GSU1805

GSU1805 has total of 34 gene neighbors in modules 102, 143
Gene neighbors (34)
Gene Common Name Description Module membership
GSU0000.1 dnaA chromosomal replication initiator protein DnaA (NCBI) 102, 316
GSU0001 dnaN DNA polymerase III, beta subunit (NCBI) 83, 102
GSU0319 GSU0319 hypothetical protein (VIMSS) 143, 332
GSU0322 gspK general secretion pathway protein K (NCBI) 143, 334
GSU0323 GSU0323 general secretion pathway protein j, putative (NCBI) 143, 334
GSU0324 GSU0324 general secretion pathway protein I, putative (NCBI) 143, 332
GSU0326 gspG general secretion pathway protein G (NCBI) 93, 143
GSU0581 GSU0581 cold-shock domain family protein (VIMSS) 102, 248
GSU1113 GSU1113 carbohydrate kinase, PfkB family (VIMSS) 87, 102
GSU1138 GSU1138 Ser/Thr protein phosphatase family protein (NCBI) 102, 207
GSU1243 coaD pantetheine-phosphate adenylyltransferase (NCBI) 143, 204
GSU1366 GSU1366 hypothetical protein (VIMSS) 143, 338
GSU1424 GSU1424 hypothetical protein (VIMSS) 31, 102
GSU1524 pcm protein-L-isoaspartate O-methyltransferase (NCBI) 102, 192
GSU1729 GSU1729 phenylacetate-CoA ligase (NCBI) 143, 255
GSU1731 livG branched-chain amino acid ABC transporter, ATP-binding protein (NCBI) 143, 255
GSU1755 pyrD dihydroorotate dehydrogenase (NCBI) 143, 174
GSU1801 GSU1801 CBS domain protein (VIMSS) 143, 168
GSU1805 glmM phosphoglucosamine mutase (NCBI) 102, 143
GSU1814 GSU1814 septum formation initiator family protein (NCBI) 31, 102
GSU1907 pssA CDP-diacylglycerol--serineO-phosphatidyltransferase (NCBI) 102, 248
GSU1914 GSU1914 membrane-associated zinc metalloprotease, putative (VIMSS) 67, 102
GSU1946 GSU1946 hypothetical protein (VIMSS) 102, 254
GSU2109 GSU2109 hypothetical protein (VIMSS) 102, 324
GSU2110 GSU2110 hypothetical protein (VIMSS) 102, 249
GSU2111 GSU2111 hypothetical protein (VIMSS) 102, 249
GSU2235 GSU2235 endoribonuclease L-PSP, putative (VIMSS) 102, 324
GSU2236 relA GTP pyrophosphokinase (NCBI) 102, 306
GSU2246 GSU2246 polysaccharide biosynthesis domain protein (VIMSS) 102, 330
GSU2248 GSU2248 conserved hypothetical protein (VIMSS) 87, 102
GSU2305 GSU2305 peptidoglycan-associated lipoprotein (VIMSS) 111, 143
GSU2521 GSU2521 conserved hypothetical protein (VIMSS) 83, 143
GSU2615 GSU2615 TPR domain protein (VIMSS) 5, 143
GSU2616 secF protein-export membrane protein SecF (NCBI) 5, 143
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 GSU1805
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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