Organism : Pseudomonas aeruginosa | Module List :
PA2838

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2838
(Mouseover regulator name to see its description)

PA2838 is regulated by 32 influences and regulates 42 modules.
Regulators for PA2838 (32)
Regulator Module Operator
PA0163 156 tf
PA0272 156 tf
PA0564 156 tf
PA0701 156 tf
PA0828 156 tf
PA1109 156 tf
PA1347 156 tf
PA2076 156 tf
PA2547 156 tf
PA2838 156 tf
PA3594 156 tf
PA3714 156 tf
PA4806 156 tf
PA4906 156 tf
PA5293 156 tf
PA5344 156 tf
PA0032 201 tf
PA0163 201 tf
PA0701 201 tf
PA0828 201 tf
PA1351 201 tf
PA1399 201 tf
PA1998 201 tf
PA2510 201 tf
PA2696 201 tf
PA2838 201 tf
PA2848 201 tf
PA3045 201 tf
PA3381 201 tf
PA3594 201 tf
PA5293 201 tf
PA5562 201 tf
Regulated by PA2838 (42)
Module Residual Genes
12 0.41 17
16 0.50 22
25 0.40 13
50 0.41 16
104 0.52 27
105 0.43 19
118 0.44 16
132 0.44 22
156 0.44 25
172 0.45 17
177 0.45 21
180 0.41 14
197 0.50 22
199 0.46 25
201 0.42 20
211 0.44 19
215 0.53 19
235 0.48 24
267 0.48 26
283 0.51 26
285 0.47 21
289 0.48 20
307 0.47 16
317 0.44 19
330 0.48 28
333 0.50 27
343 0.45 22
359 0.44 21
372 0.52 24
407 0.46 20
434 0.51 28
439 0.44 19
446 0.45 21
459 0.48 19
471 0.41 18
476 0.42 19
481 0.46 19
486 0.47 21
526 0.47 18
534 0.45 16
536 0.51 25
545 0.46 16
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3140 2.70e-01 GaaaAgaAaAAccAA
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3141 1.90e+03 CCCGgCGC
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3230 1.20e+03 AaGGAAacACAa
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3231 2.50e+04 AaATGCATTT
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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 PA2838

PA2838 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA2838

PA2838 has total of 42 gene neighbors in modules 156, 201
Gene neighbors (42)
Gene Common Name Description Module membership
PA0029 PA0029 probable sulfate transporter (NCBI) 201, 461
PA0151 PA0151 probable TonB-dependent receptor (NCBI) 119, 156
PA0183 atsA arylsulfatase (NCBI) 201, 362
PA0189 PA0189 probable porin (NCBI) 36, 201
PA0234 PA0234 hypothetical protein (NCBI) 156, 197
PA0235 pcaK 4-hydroxybenzoate transporter PcaK (NCBI) 201, 471
PA0242 PA0242 hypothetical protein (NCBI) 156, 401
PA0435 PA0435 hypothetical protein (NCBI) 156, 445
PA0809 PA0809 probable transporter (NCBI) 156, 201
PA0819 PA0819 hypothetical protein (NCBI) 201, 516
PA0912 PA0912 hypothetical protein (NCBI) 201, 516
PA1148 toxA exotoxin A precursor (NCBI) 156, 355
PA1154 PA1154 hypothetical protein (NCBI) 156, 355
PA1253 PA1253 probable semialdehyde dehydrogenase (NCBI) 201, 439
PA1410 PA1410 probable periplasmic spermidine/putrescine-binding protein (NCBI) 104, 156
PA1491 PA1491 probable transporter (NCBI) 156, 534
PA1492 PA1492 hypothetical protein (NCBI) 156, 326
PA1497 PA1497 probable transporter (NCBI) 105, 201
PA1918 PA1918 hypothetical protein (NCBI) 201, 439
PA2213 PA2213 probable porin (NCBI) 156, 201
PA2357 msuE NADH-dependent FMN reductase MsuE (NCBI) 156, 446
PA2636 PA2636 hypothetical protein (NCBI) 201, 288
PA2689 PA2689 hypothetical protein (NCBI) 132, 201
PA2772 PA2772 hypothetical protein (NCBI) 156, 171
PA2837 PA2837 probable outer membrane protein precursor (NCBI) 201, 486
PA2838 PA2838 probable transcriptional regulator (NCBI) 156, 201
PA2880 PA2880 hypothetical protein (NCBI) 201, 407
PA2898 PA2898 hypothetical protein (NCBI) 156, 486
PA2934 PA2934 probable hydrolase (NCBI) 201, 333
PA2941 PA2941 hypothetical protein (NCBI) 156, 190
PA3058 pelG hypothetical protein (NCBI) 156, 211
PA3059 pelF hypothetical protein (NCBI) 156, 434
PA3062 pelC hypothetical protein (NCBI) 156, 434
PA3063 pelB hypothetical protein (NCBI) 156, 326
PA3298 PA3298 hypothetical protein (NCBI) 156, 211
PA3772 PA3772 hypothetical protein (NCBI) 156, 211
PA3892 PA3892 hypothetical protein (NCBI) 65, 156
PA3946 PA3946 probable two-component sensor (NCBI) 201, 446
PA3947 PA3947 probable two-component response regulator (NCBI) 201, 498
PA4095 PA4095 hypothetical protein (NCBI) 25, 156
PA4342 PA4342 probable amidase (NCBI) 201, 359
PA5387 PA5387 hypothetical protein (NCBI) 156, 180
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 PA2838
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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