Organism : Pseudomonas aeruginosa | Module List :
PA2163

hypothetical protein (NCBI)

CircVis
Functional Annotations (7)
Function System
4-alpha-glucanotransferase cog/ cog
4-alpha-glucanotransferase activity go/ molecular_function
carbohydrate metabolic process go/ biological_process
cation binding go/ molecular_function
Starch and sucrose metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
malQ tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2163
(Mouseover regulator name to see its description)

PA2163 is regulated by 62 influences and regulates 0 modules.
Regulators for PA2163 (62)
Regulator Module Operator
PA0152 318 tf
PA0167 318 tf
PA0547 318 tf
PA0610 318 tf
PA0816 318 tf
PA0877 318 tf
PA0961 318 tf
PA1128 318 tf
PA1138 318 tf
PA1283 318 tf
PA1351 318 tf
PA1374 318 tf
PA1627 318 tf
PA1663 318 tf
PA2121 318 tf
PA2469 318 tf
PA2896 318 tf
PA3006 318 tf
PA3045 318 tf
PA3124 318 tf
PA3197 318 tf
PA3363 318 tf
PA3583 318 tf
PA3596 318 tf
PA3604 318 tf
PA3879 318 tf
PA4074 318 tf
PA4184 318 tf
PA4203 318 tf
PA4581 318 tf
PA4853 318 tf
PA5483 318 tf
PA0152 533 tf
PA0547 533 tf
PA0610 533 tf
PA0831 533 tf
PA0877 533 tf
PA1138 533 tf
PA1153 533 tf
PA1223 533 tf
PA1283 533 tf
PA1347 533 tf
PA1351 533 tf
PA1374 533 tf
PA1627 533 tf
PA1663 533 tf
PA2121 533 tf
PA2469 533 tf
PA2896 533 tf
PA3006 533 tf
PA3045 533 tf
PA3122 533 tf
PA3197 533 tf
PA3363 533 tf
PA3583 533 tf
PA3604 533 tf
PA3879 533 tf
PA4074 533 tf
PA4203 533 tf
PA4581 533 tf
PA4853 533 tf
PA5483 533 tf

Warning: PA2163 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
3462 9.40e+00 gA.CgcC.GggaAAaag.ccGAac
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3463 9.40e+02 Gcc.CGGcG.CCgcC
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3878 3.30e+02 AaaAA.CTGAAC
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3879 8.10e+03 TCTCGAAA
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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 PA2163

PA2163 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
4-alpha-glucanotransferase cog/ cog
4-alpha-glucanotransferase activity go/ molecular_function
carbohydrate metabolic process go/ biological_process
cation binding go/ molecular_function
Starch and sucrose metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
malQ tigr/ tigrfam
Module neighborhood information for PA2163

PA2163 has total of 24 gene neighbors in modules 318, 533
Gene neighbors (24)
Gene Common Name Description Module membership
PA2134 PA2134 hypothetical protein (NCBI) 194, 533
PA2139 PA2139 hypothetical protein (NCBI) 161, 318
PA2142 PA2142 probable short-chain dehydrogenase (NCBI) 161, 318
PA2143 PA2143 hypothetical protein (NCBI) 318, 479
PA2144 glgP glycogen phosphorylase (NCBI) 194, 318
PA2147 katE catalase HPII (NCBI) 318, 521
PA2151 PA2151 hypothetical protein (NCBI) 161, 318
PA2152 PA2152 probable trehalose synthase (NCBI) 194, 533
PA2153 glgB glycogen branching enzyme (NCBI) 318, 533
PA2156 PA2156 hypothetical protein (NCBI) 161, 318
PA2157 PA2157 hypothetical protein (NCBI) 161, 533
PA2158 PA2158 probable alcohol dehydrogenase (Zn-dependent) (NCBI) 318, 533
PA2159 PA2159 hypothetical protein (NCBI) 318, 533
PA2160 PA2160 probable glycosyl hydrolase (NCBI) 318, 533
PA2161 PA2161 hypothetical protein (NCBI) 318, 533
PA2162 PA2162 probable glycosyl hydrolase (NCBI) 318, 533
PA2163 PA2163 hypothetical protein (NCBI) 318, 533
PA2164 PA2164 probable glycosyl hydrolase (NCBI) 318, 533
PA2165 PA2165 glycogen synthase (NCBI) 318, 533
PA2169 PA2169 hypothetical protein (NCBI) 194, 533
PA2171 PA2171 hypothetical protein (NCBI) 194, 318
PA2172 PA2172 hypothetical protein (NCBI) 194, 318
PA2173 PA2173 hypothetical protein (NCBI) 479, 533
PA4171 PA4171 probable protease (NCBI) 194, 318
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 PA2163
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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