Organism : Pseudomonas aeruginosa | Module List :
PA0238

hypothetical protein (NCBI)

CircVis
Functional Annotations (1)
Function System
Sugar phosphate isomerases/epimerases cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0238
(Mouseover regulator name to see its description)

PA0238 is regulated by 40 influences and regulates 0 modules.
Regulators for PA0238 (40)
Regulator Module Operator
PA0032 180 tf
PA0218 180 tf
PA0306 180 tf
PA0828 180 tf
PA1145 180 tf
PA1197 180 tf
PA1264 180 tf
PA1399 180 tf
PA1467 180 tf
PA1980 180 tf
PA2838 180 tf
PA3381 180 tf
PA3420 180 tf
PA3594 180 tf
PA3714 180 tf
PA4755 180 tf
PA4806 180 tf
PA5344 180 tf
PA5562 180 tf
PA0032 471 tf
PA0056 471 tf
PA0167 471 tf
PA0207 471 tf
PA0547 471 tf
PA0828 471 tf
PA1145 471 tf
PA1347 471 tf
PA1351 471 tf
PA1467 471 tf
PA1826 471 tf
PA1980 471 tf
PA2093 471 tf
PA2838 471 tf
PA3045 471 tf
PA3381 471 tf
PA3420 471 tf
PA3594 471 tf
PA3714 471 tf
PA4341 471 tf
PA4769 471 tf

Warning: PA0238 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
3188 7.60e+01 TGgcGgtTtC.GCa
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3189 4.50e+03 ACAaGaAatt
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3758 6.10e-01 CgAacAaaAcaacA
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3759 1.30e+03 AcTGccgATCgaTT
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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 PA0238

PA0238 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Sugar phosphate isomerases/epimerases cog/ cog
Module neighborhood information for PA0238

PA0238 has total of 29 gene neighbors in modules 180, 471
Gene neighbors (29)
Gene Common Name Description Module membership
PA0226 PA0226 probable CoA transferase, subunit A (NCBI) 471, 500
PA0227 PA0227 probable CoA transferase, subunit B (NCBI) 471, 500
PA0228 pcaF acetyl-CoA acetyltransferase (NCBI) 471, 500
PA0235 pcaK 4-hydroxybenzoate transporter PcaK (NCBI) 201, 471
PA0237 PA0237 probable oxidoreductase (NCBI) 180, 471
PA0238 PA0238 hypothetical protein (NCBI) 180, 471
PA0247 pobA 4-hydroxybenzoate 3-monooxygenase (NCBI) 471, 536
PA0348 PA0348 hypothetical protein (NCBI) 136, 471
PA0812 PA0812 hypothetical protein (NCBI) 211, 471
PA1252 PA1252 probable L-malate dehydrogenase (NCBI) 180, 295
PA1314 PA1314 hypothetical protein (NCBI) 471, 475
PA1498 pykF pyruvate kinase (NCBI) 180, 532
PA1952 PA1952 hypothetical protein (NCBI) 105, 180
PA2130 cupA3 usher CupA3 (NCBI) 439, 471
PA2131 cupA4 fimbrial subunit CupA4 (NCBI) 439, 471
PA2132 cupA5 chaperone CupA5 (NCBI) 439, 471
PA2803 PA2803 hypothetical protein (NCBI) 25, 471
PA2878 PA2878 hypothetical protein (NCBI) 180, 288
PA3714 PA3714 probable two-component response regulator (NCBI) 180, 326
PA4549 fimT type 4 fimbrial biogenesis protein FimT (NCBI) 80, 471
PA4589 PA4589 probable outer membrane protein precursor (NCBI) 246, 471
PA4814 fadH2 2,4-dienoyl-CoA reductase FadH2 (NCBI) 180, 439
PA4818 PA4818 hypothetical protein (NCBI) 180, 463
PA4819 PA4819 probable glycosyl transferase (NCBI) 180, 463
PA4994 PA4994 probable acyl-CoA dehydrogenase (NCBI) 471, 532
PA5031 PA5031 probable short chain dehydrogenase (NCBI) 180, 471
PA5327 PA5327 probable oxidoreductase (NCBI) 180, 507
PA5379 sdaB L-serine dehydratase (NCBI) 180, 470
PA5387 PA5387 hypothetical protein (NCBI) 156, 180
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 PA0238
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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