Organism : Pseudomonas aeruginosa | Module List :
PA0890 aotM

arginine/ornithine transport protein AotM (NCBI)

CircVis
Functional Annotations (9)
Function System
ABC-type arginine/histidine transport system, permease component cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transporter activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
transport go/ biological_process
Gram-negative-bacterium-type cell wall go/ cellular_component
integral to membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
HEQRo_perm_3TM tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0890
(Mouseover regulator name to see its description)

PA0890 is regulated by 39 influences and regulates 41 modules.
Regulators for PA0890 aotM (39)
Regulator Module Operator
PA0179 353 tf
PA0275 353 tf
PA0890 353 tf
PA0893 353 tf
PA0961 353 tf
PA1945 353 tf
PA2622 353 tf
PA3002 353 tf
PA3804 353 tf
PA3948 353 tf
PA4269 353 tf
PA4275 353 tf
PA4530 353 tf
PA4547 353 tf
PA4906 353 tf
PA5239 353 tf
PA5253 353 tf
PA5342 353 tf
PA5550 353 tf
PA5562 353 tf
PA0475 160 tf
PA0763 160 tf
PA0890 160 tf
PA0893 160 tf
PA1159 160 tf
PA1359 160 tf
PA1374 160 tf
PA1776 160 tf
PA2859 160 tf
PA2897 160 tf
PA3002 160 tf
PA3804 160 tf
PA3965 160 tf
PA4238 160 tf
PA4269 160 tf
PA4270 160 tf
PA4547 160 tf
PA5166 160 tf
PA5562 160 tf

Warning: PA0890 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
3148 1.10e+03 TAcAATGC
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3149 2.60e+03 CATCGA
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3530 1.20e+02 taG.A.cg.tTCGAA
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3531 4.60e+03 ca.ccgGcAG.AggtgaAcgcGtt
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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 PA0890

PA0890 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
ABC-type arginine/histidine transport system, permease component cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transporter activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
transport go/ biological_process
Gram-negative-bacterium-type cell wall go/ cellular_component
integral to membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
HEQRo_perm_3TM tigr/ tigrfam
Module neighborhood information for PA0890

PA0890 has total of 33 gene neighbors in modules 160, 353
Gene neighbors (33)
Gene Common Name Description Module membership
PA0549 PA0549 hypothetical protein (NCBI) 353, 396
PA0593 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase (NCBI) 37, 160
PA0594 surA peptidyl-prolyl cis-trans isomerase SurA (NCBI) 121, 160
PA0889 aotQ arginine/ornithine transport protein AotQ (NCBI) 353, 396
PA0890 aotM arginine/ornithine transport protein AotM (NCBI) 160, 353
PA0891 PA0891 hypothetical protein (NCBI) 150, 160
PA0892 aotP arginine/ornithine transport protein AotP (NCBI) 150, 160
PA0893 argR transcriptional regulator ArgR (NCBI) 60, 160
PA0955 PA0955 hypothetical protein (NCBI) 160, 427
PA1767 PA1767 hypothetical protein (NCBI) 160, 350
PA2986 PA2986 hypothetical protein (NCBI) 353, 442
PA2987 PA2987 probable ATP-binding component of ABC transporter (NCBI) 91, 353
PA3107 metZ O-succinylhomoserine sulfhydrylase (NCBI) 150, 160
PA3626 PA3626 tRNA pseudouridine synthase D (NCBI) 207, 353
PA3652 uppS undecaprenyl pyrophosphate synthetase (NCBI) 270, 353
PA3799 engA GTP-binding protein EngA (NCBI) 270, 353
PA3802 hisS histidyl-tRNA synthetase (NCBI) 150, 160
PA3803 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (NCBI) 150, 160
PA3827 PA3827 hypothetical protein (NCBI) 131, 353
PA4447 hisC1 histidinol-phosphate aminotransferase (NCBI) 174, 353
PA4448 hisD histidinol dehydrogenase (NCBI) 306, 353
PA4485 PA4485 hypothetical protein (NCBI) 14, 353
PA5001 PA5001 hypothetical protein (NCBI) 270, 353
PA5002 PA5002 hypothetical protein (NCBI) 270, 353
PA5109 PA5109 hypothetical protein (NCBI) 14, 353
PA5140 hisF1 imidazole glycerol phosphate synthase subunit HisF (NCBI) 204, 353
PA5147 mutY A / G specific adenine glycosylase (NCBI) 150, 160
PA5149 PA5149 hypothetical protein (NCBI) 20, 353
PA5203 gshA glutamate--cysteine ligase (NCBI) 353, 389
PA5222 PA5222 hypothetical protein (NCBI) 353, 499
PA5236 PA5236 hypothetical protein (NCBI) 14, 353
PA5340 PA5340 hypothetical protein (NCBI) 42, 160
PA5549 glmS D-fructose-6-phosphate amidotransferase (NCBI) 270, 353
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 PA0890
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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