Organism : Pseudomonas aeruginosa | Module List :
PA3667

probable pyridoxal-phosphate dependent enzyme (NCBI)

CircVis
Functional Annotations (5)
Function System
Selenocysteine lyase cog/ cog
metabolic process go/ biological_process
transaminase activity go/ molecular_function
selenocysteine lyase activity go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3667
(Mouseover regulator name to see its description)

PA3667 is regulated by 35 influences and regulates 0 modules.
Regulators for PA3667 (35)
Regulator Module Operator
PA0393 130 tf
PA0455 130 tf
PA0893 130 tf
PA3002 130 tf
PA3563 130 tf
PA3711 130 tf
PA3804 130 tf
PA4052 130 tf
PA4269 130 tf
PA4547 130 tf
PA4745 130 tf
PA4755 130 tf
PA5166 130 tf
PA0393 202 tf
PA0455 202 tf
PA0890 202 tf
PA0893 202 tf
PA1097 202 tf
PA1269 202 tf
PA1283 202 tf
PA1347 202 tf
PA1526 202 tf
PA1663 202 tf
PA1776 202 tf
PA1850 202 tf
PA1864 202 tf
PA2016 202 tf
PA2432 202 tf
PA2586 202 tf
PA3002 202 tf
PA3126 202 tf
PA3285 202 tf
PA3804 202 tf
PA4547 202 tf
PA5125 202 tf

Warning: PA3667 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
3090 5.60e+02 ATtATgcC
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3091 1.60e+04 CTGAAAAA
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3232 2.00e-03 AcTcCTGCtgAACccggcct
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3233 5.80e+02 tC.G.CgctacGccg
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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 PA3667

PA3667 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Selenocysteine lyase cog/ cog
metabolic process go/ biological_process
transaminase activity go/ molecular_function
selenocysteine lyase activity go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
Module neighborhood information for PA3667

PA3667 has total of 35 gene neighbors in modules 130, 202
Gene neighbors (35)
Gene Common Name Description Module membership
PA0552 pgk phosphoglycerate kinase (NCBI) 130, 260
PA0589 glpE thiosulfate sulfurtransferase (NCBI) 202, 464
PA0591 PA0591 hypothetical protein (NCBI) 202, 464
PA0769 PA0769 hypothetical protein (NCBI) 129, 202
PA0770 rnc ribonuclease III (NCBI) 129, 202
PA0773 pdxJ pyridoxal phosphate biosynthetic protein (NCBI) 202, 387
PA0859 PA0859 hypothetical protein (NCBI) 117, 130
PA0919 PA0919 hypothetical protein (NCBI) 202, 384
PA0920 PA0920 hypothetical protein (NCBI) 202, 384
PA0921 PA0921 hypothetical protein (NCBI) 202, 384
PA1178 oprH PhoP/Q and low Mg2+ inducible outer membrane protein H1 precursor (NCBI) 202, 543
PA1179 phoP two-component response regulator PhoP (NCBI) 202, 543
PA1180 phoQ two-component sensor PhoQ (NCBI) 91, 202
PA1181 PA1181 hypothetical protein (NCBI) 202, 320
PA1343 PA1343 hypothetical protein (NCBI) 202, 226
PA1527 PA1527 hypothetical protein (NCBI) 202, 522
PA3047 PA3047 probable D-alanyl-D-alanine carboxypeptidase (NCBI) 91, 130
PA3170 PA3170 N-ethylammeline chlorohydrolase (NCBI) 86, 130
PA3667 PA3667 probable pyridoxal-phosphate dependent enzyme (NCBI) 130, 202
PA3668 PA3668 hypothetical protein (NCBI) 130, 202
PA4011 PA4011 hypothetical protein (NCBI) 130, 396
PA4019 PA4019 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (NCBI) 6, 202
PA4020 mpl UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase (NCBI) 6, 202
PA4049 PA4049 hypothetical protein (NCBI) 91, 202
PA4054 ribB bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein (NCBI) 130, 511
PA4055 ribC riboflavin synthase subunit alpha (NCBI) 77, 130
PA4284 recB exodeoxyribonuclease V beta chain (NCBI) 49, 130
PA4662 murI glutamate racemase (NCBI) 130, 426
PA4663 moeB molybdopterin biosynthesis protein MoeB (NCBI) 130, 426
PA4728 folK 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase (NCBI) 130, 396
PA4951 orn oligoribonuclease (NCBI) 51, 202
PA4966 PA4966 hypothetical protein (NCBI) 49, 130
PA5165 PA5165 probable two-component sensor (NCBI) 49, 130
PA5166 PA5166 probable two-component response regulator (NCBI) 130, 540
PA5429 aspA aspartate ammonia-lyase (NCBI) 179, 202
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 PA3667
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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