Organism : Pseudomonas aeruginosa | Module List :
PA2227

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2227
(Mouseover regulator name to see its description)

PA2227 is regulated by 38 influences and regulates 19 modules.
Regulators for PA2227 (38)
Regulator Module Operator
PA0207 385 tf
PA0243 385 tf
PA0393 385 tf
PA0701 385 tf
PA0979 385 tf
PA1067 385 tf
PA1153 385 tf
PA1359 385 tf
PA1961 385 tf
PA2100 385 tf
PA2206 385 tf
PA2227 385 tf
PA2736 385 tf
PA3045 385 tf
PA3133 385 tf
PA3711 385 tf
PA0233 188 tf
PA0535 188 tf
PA0791 188 tf
PA0873 188 tf
PA1229 188 tf
PA1261 188 tf
PA1359 188 tf
PA1363 188 tf
PA2054 188 tf
PA2076 188 tf
PA2227 188 tf
PA2376 188 tf
PA2736 188 tf
PA3045 188 tf
PA3699 188 tf
PA3711 188 tf
PA3757 188 tf
PA3879 188 tf
PA4077 188 tf
PA4269 188 tf
PA5337 188 tf
PA5438 188 tf
Regulated by PA2227 (19)
Module Residual Genes
25 0.40 13
80 0.43 20
168 0.45 21
188 0.49 22
219 0.27 12
231 0.51 26
254 0.44 24
297 0.43 17
298 0.21 15
300 0.44 18
303 0.46 18
324 0.51 27
348 0.50 30
385 0.43 19
445 0.52 21
476 0.42 19
485 0.35 15
503 0.40 12
508 0.35 13
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3204 1.80e-06 atTccaAAAtaagata.tt
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3205 2.60e-02 a.aaAttgAct.TtA
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3594 6.60e-04 tTt.t.ttttcagT.aAtgtcatg
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3595 1.10e+01 ttgaAGTT
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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 PA2227

PA2227 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for PA2227

PA2227 has total of 36 gene neighbors in modules 188, 385
Gene neighbors (36)
Gene Common Name Description Module membership
PA0642 PA0642 hypothetical protein (NCBI) 11, 188
PA0643 PA0643 hypothetical protein (NCBI) 188, 297
PA0644 PA0644 hypothetical protein (NCBI) 188, 297
PA0645 PA0645 hypothetical protein (NCBI) 188, 297
PA0646 PA0646 hypothetical protein (NCBI) 11, 188
PA0647 PA0647 hypothetical protein (NCBI) 11, 188
PA0715 PA0715 hypothetical protein (NCBI) 188, 485
PA0716 PA0716 hypothetical protein (NCBI) 188, 485
PA0826 PA0826 hypothetical protein (NCBI) 188, 231
PA0980 PA0980 hypothetical protein (NCBI) 188, 231
PA0981 PA0981 hypothetical protein (NCBI) 231, 385
PA0992 cupC1 fimbrial subunit CupC1 (NCBI) 231, 385
PA0993 cupC2 chaperone CupC2 (NCBI) 25, 385
PA1152 PA1152 hypothetical protein (NCBI) 188, 231
PA1371 PA1371 hypothetical protein (NCBI) 188, 476
PA1381 PA1381 hypothetical protein (NCBI) 254, 385
PA1382 PA1382 probable type II secretion system protein (NCBI) 303, 385
PA1384 galE UDP-glucose 4-epimerase (NCBI) 254, 385
PA1385 PA1385 probable glycosyl transferase (NCBI) 254, 385
PA1386 PA1386 probable ATP-binding component of ABC transporter (NCBI) 254, 385
PA1387 PA1387 hypothetical protein (NCBI) 324, 385
PA1388 PA1388 hypothetical protein (NCBI) 324, 385
PA1389 PA1389 probable glycosyl transferase (NCBI) 324, 385
PA1393 cysC adenosine 5'-phosphosulfate (APS) kinase (NCBI) 254, 385
PA2037 PA2037 hypothetical protein (NCBI) 188, 231
PA2222 PA2222 hypothetical protein (NCBI) 188, 476
PA2223 PA2223 hypothetical protein (NCBI) 188, 476
PA2224 PA2224 hypothetical protein (NCBI) 188, 385
PA2225 PA2225 hypothetical protein (NCBI) 188, 385
PA2226 PA2226 hypothetical protein (NCBI) 188, 385
PA2227 PA2227 probable transcriptional regulator (NCBI) 188, 385
PA2228 PA2228 hypothetical protein (NCBI) 188, 385
PA2791 PA2791 hypothetical protein (NCBI) 340, 385
PA2794 PA2794 hypothetical protein (NCBI) 152, 188
PA3045 PA3045 probable two-component response regulator (NCBI) 105, 385
PA5264 PA5264 hypothetical protein (NCBI) 188, 231
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 PA2227
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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