Organism : Pseudomonas aeruginosa | Module List :
PA1072 braE

branched-chain amino acid transport protein BraE (NCBI)

CircVis
Functional Annotations (5)
Function System
ABC-type branched-chain amino acid transport system, permease component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1072
(Mouseover regulator name to see its description)

PA1072 is regulated by 68 influences and regulates 0 modules.
Regulators for PA1072 braE (68)
Regulator Module Operator
PA0610 336 tf
PA1015 336 tf
PA1159 336 tf
PA1285 336 tf
PA1335 336 tf
PA1359 336 tf
PA1403 336 tf
PA1467 336 tf
PA1653 336 tf
PA1759 336 tf
PA1760 336 tf
PA1850 336 tf
PA1853 336 tf
PA2016 336 tf
PA2020 336 tf
PA2484 336 tf
PA2591 336 tf
PA3921 336 tf
PA4021 336 tf
PA4070 336 tf
PA4354 336 tf
PA4755 336 tf
PA4787 336 tf
PA5380 336 tf
PA0243 193 tf
PA0610 193 tf
PA0893 193 tf
PA1099 193 tf
PA1159 193 tf
PA1241 193 tf
PA1335 193 tf
PA1347 193 tf
PA1359 193 tf
PA1544 193 tf
PA1633 193 tf
PA1754 193 tf
PA1759 193 tf
PA1760 193 tf
PA1776 193 tf
PA2016 193 tf
PA2020 193 tf
PA2047 193 tf
PA2054 193 tf
PA2056 193 tf
PA2121 193 tf
PA2320 193 tf
PA2376 193 tf
PA2387 193 tf
PA2577 193 tf
PA2846 193 tf
PA2896 193 tf
PA3027 193 tf
PA3782 193 tf
PA3965 193 tf
PA4269 193 tf
PA4270 193 tf
PA4296 193 tf
PA4436 193 tf
PA4755 193 tf
PA4778 193 tf
PA4787 193 tf
PA4853 193 tf
PA5125 193 tf
PA5255 193 tf
PA5261 193 tf
PA5308 193 tf
PA5337 193 tf
PA5380 193 tf

Warning: PA1072 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
3214 7.50e-05 aCaAgAAcAAt
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3215 1.60e+04 CtCTAcaCTGttCcG
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3498 1.20e+01 AtaACAAC
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3499 9.40e+03 GATAAA
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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 PA1072

PA1072 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
ABC-type branched-chain amino acid transport system, permease component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
Module neighborhood information for PA1072

PA1072 has total of 35 gene neighbors in modules 193, 336
Gene neighbors (35)
Gene Common Name Description Module membership
PA0300 spuD polyamine transport protein (NCBI) 15, 193
PA0958 oprD Basic amino acid, basic peptide and imipenem outer membrane porin OprD precursor (NCBI) 193, 234
PA1070 braG branched-chain amino acid transport protein BraG (NCBI) 193, 336
PA1071 braF branched-chain amino acid transport protein BraF (NCBI) 193, 336
PA1072 braE branched-chain amino acid transport protein BraE (NCBI) 193, 336
PA1073 braD branched-chain amino acid transport protein BraD (NCBI) 193, 234
PA1074 braC branched-chain amino acid transport protein BraC (NCBI) 15, 193
PA1337 ansB glutaminase-asparaginase (NCBI) 15, 336
PA1338 ggt gamma-glutamyltranspeptidase precursor (NCBI) 193, 336
PA1339 PA1339 probable ATP-binding component of ABC transporter (NCBI) 15, 336
PA1340 PA1340 probable permease of ABC transporter (NCBI) 193, 336
PA1341 PA1341 probable permease of ABC transporter (NCBI) 193, 336
PA1342 PA1342 probable binding protein component of ABC transporter (NCBI) 15, 193
PA1818 PA1818 probable Orn/Arg/Lys decarboxylase (NCBI) 193, 491
PA1984 PA1984 probable aldehyde dehydrogenase (NCBI) 239, 336
PA3836 PA3836 hypothetical protein (NCBI) 193, 234
PA3837 PA3837 probable permease of ABC transporter (NCBI) 193, 234
PA3838 PA3838 probable ATP-binding component of ABC transporter (NCBI) 193, 234
PA4023 PA4023 probable transport protein (NCBI) 239, 336
PA4024 eutB ethanolamine ammonia-lyase large subunit (NCBI) 239, 336
PA4025 PA4025 ethanolamine ammonia-lyase small subunit (NCBI) 239, 336
PA4606 PA4606 hypothetical protein (NCBI) 193, 234
PA5112 estA esterase EstA (NCBI) 193, 388
PA5152 PA5152 probable ATP-binding component of ABC transporter (NCBI) 193, 234
PA5153 PA5153 probable periplasmic binding protein (NCBI) 193, 239
PA5154 PA5154 probable permease of ABC transporter (NCBI) 193, 234
PA5155 PA5155 probable permease of ABC transporter (NCBI) 193, 234
PA5167 PA5167 probable c4-dicarboxylate-binding protein (NCBI) 193, 491
PA5448 wbpY glycosyltransferase WbpY (NCBI) 215, 336
PA5449 wbpX glycosyltransferase WbpX (NCBI) 215, 336
PA5450 wzt ABC subunit of A-band LPS efflux transporter (NCBI) 215, 336
PA5451 wzm membrane subunit of A-band LPS efflux transporter (NCBI) 215, 336
PA5452 wbpW phosphomannose isomerase/GDP-mannose WbpW (NCBI) 215, 336
PA5453 gmd GDP-mannose 4,6-dehydratase (NCBI) 215, 336
PA5454 rmd oxidoreductase Rmd (NCBI) 215, 336
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 PA1072
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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