Organism : Pseudomonas aeruginosa | Module List :
PA0243

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0243
(Mouseover regulator name to see its description)

PA0243 is regulated by 15 influences and regulates 7 modules.
Regulators for PA0243 (15)
Regulator Module Operator
PA0243 72 tf
PA2076 72 tf
PA2802 72 tf
PA2896 72 tf
PA2957 72 tf
PA3341 72 tf
PA3477 72 tf
PA3699 72 tf
PA4451 72 tf
PA4745 72 tf
PA4764 72 tf
PA4769 72 tf
PA4853 72 tf
PA5337 72 tf
PA5344 72 tf

Warning: PA0243 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
2976 1.20e+04 ATcA.c.CCaa
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2977 1.80e+04 ct.cCatcC.cttCC.T.cCG.A
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3268 3.90e+00 ATAATcGggCGctct
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3269 1.20e+04 aaTgcgtgatccGaaAtAaTC
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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 PA0243

PA0243 is enriched for 5 functions in 3 categories.
Module neighborhood information for PA0243

PA0243 has total of 48 gene neighbors in modules 72, 220
Gene neighbors (48)
Gene Common Name Description Module membership
PA0168 PA0168 hypothetical protein (NCBI) 220, 316
PA0243 PA0243 probable transcriptional regulator (NCBI) 72, 220
PA0307 PA0307 hypothetical protein (NCBI) 72, 245
PA0308 PA0308 hypothetical protein (NCBI) 220, 490
PA0351 PA0351 hypothetical protein (NCBI) 72, 220
PA0363 coaD phosphopantetheine adenylyltransferase (NCBI) 72, 178
PA0433 PA0433 hypothetical protein (NCBI) 187, 220
PA0487 PA0487 probable molybdenum transport regulator (NCBI) 220, 523
PA0538 dsbB disulfide bond formation protein (NCBI) 220, 498
PA0662 argC N-acetyl-gamma-glutamyl-phosphate reductase (NCBI) 72, 544
PA0663 PA0663 hypothetical protein (NCBI) 72, 544
PA0664 PA0664 hypothetical protein (NCBI) 72, 544
PA0846 PA0846 putative sulfate transport protein CysZ (NCBI) 117, 220
PA0868 PA0868 hypothetical protein (NCBI) 72, 220
PA0946 PA0946 hypothetical protein (NCBI) 123, 220
PA1047 PA1047 probable esterase (NCBI) 220, 420
PA1263 PA1263 hypothetical protein (NCBI) 9, 72
PA1315 PA1315 probable transcriptional regulator (NCBI) 220, 438
PA1357 PA1357 hypothetical protein (NCBI) 72, 220
PA1398 PA1398 hypothetical protein (NCBI) 220, 229
PA1558 PA1558 hypothetical protein (NCBI) 220, 457
PA1862 modB molybdenum transport protein ModB (NCBI) 220, 263
PA2798 PA2798 probable two-component response regulator (NCBI) 72, 195
PA2802 PA2802 probable transcriptional regulator (NCBI) 72, 139
PA2823 PA2823 hypothetical protein (NCBI) 220, 315
PA2832 tpm thiopurine methyltransferase (NCBI) 70, 220
PA2900 PA2900 probable outer membrane protein precursor (NCBI) 8, 72
PA2979 kdsB 3-deoxy-manno-octulosonate cytidylyltransferase (NCBI) 72, 165
PA3004 PA3004 purine nucleoside phosphorylase (NCBI) 165, 220
PA3005 nagZ beta-hexosaminidase (NCBI) 72, 165
PA3033 PA3033 hypothetical protein (NCBI) 117, 220
PA3034 PA3034 probable transcriptional regulator (NCBI) 41, 220
PA3453 PA3453 hypothetical protein (NCBI) 58, 72
PA3463 PA3463 hypothetical protein (NCBI) 72, 229
PA3585 glpM membrane protein GlpM (NCBI) 72, 114
PA3854 PA3854 hypothetical protein (NCBI) 72, 117
PA3855 PA3855 hypothetical protein (NCBI) 220, 268
PA3859 PA3859 carboxylesterase (NCBI) 220, 225
PA3887 nhaP Na+/H+ antiporter NhaP (NCBI) 220, 490
PA3895 PA3895 probable transcriptional regulator (NCBI) 220, 268
PA3896 PA3896 probable 2-hydroxyacid dehydrogenase (NCBI) 220, 374
PA4339 PA4339 probable phospholipase (NCBI) 20, 220
PA4548 PA4548 probable D-amino acid oxidase (NCBI) 8, 220
PA5085 PA5085 probable transcriptional regulator (NCBI) 220, 266
PA5175 cysQ CysQ protein (NCBI) 220, 321
PA5199 envZ two-component sensor EnvZ (NCBI) 220, 253
PA5370 PA5370 probable major facilitator superfamily (MFS) transporter (NCBI) 58, 220
PA5529 PA5529 probable sodium/proton antiporter (NCBI) 220, 422
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 PA0243
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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