Organism : Geobacter sulfurreducens | Module List :
GSU3323 ppk

polyphosphate kinase (NCBI)

CircVis
Functional Annotations (7)
Function System
Polyphosphate kinase cog/ cog
polyphosphate biosynthetic process go/ biological_process
polyphosphate kinase activity go/ molecular_function
polyphosphate kinase complex go/ cellular_component
Oxidative phosphorylation kegg/ kegg pathway
RNA degradation kegg/ kegg pathway
poly_P_kin tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3323
(Mouseover regulator name to see its description)

GSU3323 is regulated by 16 influences and regulates 0 modules.
Regulators for GSU3323 ppk (16)
Regulator Module Operator
GSU0041 131 tf
GSU1495 131 tf
GSU1569 131 tf
GSU2964 131 tf
GSU2987 131 tf
GSU3324 131 tf
GSU3370 131 tf
GSU0063 260 tf
GSU0147 260 tf
GSU0359 260 tf
GSU1495 260 tf
GSU2033 260 tf
GSU2041 260 tf
GSU2571 260 tf
GSU3087 260 tf
GSU3370 260 tf

Warning: GSU3323 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
2422 1.60e+02 gTTtTtggAtGgAtT
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2423 6.20e+03 cTTcaCgTt.cccG
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2680 2.00e-02 gTGGCggTgCcGGc
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2681 2.10e+01 AAACttcAtgtAaaatagcGg
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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 GSU3323

GSU3323 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Polyphosphate kinase cog/ cog
polyphosphate biosynthetic process go/ biological_process
polyphosphate kinase activity go/ molecular_function
polyphosphate kinase complex go/ cellular_component
Oxidative phosphorylation kegg/ kegg pathway
RNA degradation kegg/ kegg pathway
poly_P_kin tigr/ tigrfam
Module neighborhood information for GSU3323

GSU3323 has total of 36 gene neighbors in modules 131, 260
Gene neighbors (36)
Gene Common Name Description Module membership
GSU0011 GSU0011 ABC transporter, ATP-binding protein (VIMSS) 131, 159
GSU0568 GSU0568 hypothetical protein (VIMSS) 47, 260
GSU0623 GSU0623 glycosyl transferase, group 2 family protein (VIMSS) 131, 201
GSU0624 GSU0624 glycosyl transferase, group 1 family protein (VIMSS) 131, 226
GSU0759 GSU0759 hypothetical protein (VIMSS) 260, 278
GSU0933 upp uracil phosphoribosyltransferase (NCBI) 145, 260
GSU0954 GSU0954 conserved hypothetical protein (VIMSS) 260, 338
GSU1073 GSU1073 conserved hypothetical protein (VIMSS) 35, 260
GSU1074 GSU1074 conserved hypothetical protein TIGR01033 (VIMSS) 31, 260
GSU1077 ruvB Holliday junction DNA helicase RuvB (NCBI) 208, 260
GSU1078 GSU1078 chromosomal replication initiator protein DnaA, truncation (NCBI) 226, 260
GSU1287 GSU1287 methyl accepting chemotaxis protein, putative (VIMSS) 8, 131
GSU1327 GSU1327 homocysteine S-methyltransferase domain protein (VIMSS) 79, 260
GSU1354 GSU1354 plasmid stabilization system family protein (NCBI) 159, 260
GSU1437 GSU1437 peptidase, M48 family (NCBI) 260, 301
GSU1449 GSU1449 hypothetical protein (VIMSS) 87, 260
GSU1480 GSU1480 drug resistance transporter, EmrB/QacA family (VIMSS) 131, 226
GSU1481 GSU1481 multidrug resistance protein, putative (VIMSS) 131, 204
GSU1674 GSU1674 hypothetical protein (VIMSS) 260, 338
GSU1695 thrC threonine synthase (NCBI) 131, 196
GSU1802 GSU1802 YjeF family protein (VIMSS) 260, 306
GSU1807 GSU1807 conserved hypothetical protein TIGR00159 (VIMSS) 131, 260
GSU2000 miaA tRNA delta(2)-isopentenylpyrophosphate transferase (NCBI) 34, 260
GSU2225 b2511 GTP-binding protein Era, putative (NCBI) 198, 260
GSU2240 galE UDP-glucose 4-epimerase (NCBI) 131, 201
GSU2242 GSU2242 heptosyltransferase family protein (VIMSS) 131, 176
GSU2244 GSU2244 glycosyl transferase, group 2 family protein (VIMSS) 131, 301
GSU2249 GSU2249 hypothetical protein (VIMSS) 67, 131
GSU2256 GSU2256 ADP-heptose--LPS heptosyltransferase II, putative (VIMSS) 131, 277
GSU2298 GSU2298 hypothetical protein (VIMSS) 131, 260
GSU2378 trpF N-(5'phosphoribosyl)anthranilate isomerase (NCBI) 131, 196
GSU2383 trpE anthranilate synthase component I (NCBI) 131, 196
GSU3148 GSU3148 sensor histidine kinase (VIMSS) 84, 260
GSU3183 GSU3183 hypothetical protein (VIMSS) 191, 260
GSU3282 GSU3282 siroheme synthase, N-terminal domain protein (NCBI) 260, 335
GSU3323 ppk polyphosphate kinase (NCBI) 131, 260
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 GSU3323
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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