Organism : Pseudomonas aeruginosa | Module List :
PA0253

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0253
(Mouseover regulator name to see its description)

PA0253 is regulated by 42 influences and regulates 12 modules.
Regulators for PA0253 (42)
Regulator Module Operator
PA0207 181 tf
PA0253 181 tf
PA0652 181 tf
PA0961 181 tf
PA1067 181 tf
PA1201 181 tf
PA1241 181 tf
PA1422 181 tf
PA1884 181 tf
PA2121 181 tf
PA2859 181 tf
PA2957 181 tf
PA3135 181 tf
PA3594 181 tf
PA3604 181 tf
PA3622 181 tf
PA4196 181 tf
PA4451 181 tf
PA4581 181 tf
PA4764 181 tf
PA4890 181 tf
PA5253 181 tf
PA5342 181 tf
PA5365 181 tf
PA5550 181 tf
PA0037 351 tf
PA0152 351 tf
PA0253 351 tf
PA0831 351 tf
PA1241 351 tf
PA1290 351 tf
PA1630 351 tf
PA2115 351 tf
PA2270 351 tf
PA2447 351 tf
PA2510 351 tf
PA2921 351 tf
PA3322 351 tf
PA3604 351 tf
PA4451 351 tf
PA4890 351 tf
PA5356 351 tf

Warning: PA0253 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
3190 9.80e-03 GgTAGAaTcGCGgcC.T.
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3191 1.80e+00 GTCg.A.aaagcaGGAgC.AC
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3526 2.00e-03 CgcCG.TcCgcCAt.CcttgtaG
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3527 6.60e+00 tTcG.CaAcGC
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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 PA0253

PA0253 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA0253

PA0253 has total of 50 gene neighbors in modules 181, 351
Gene neighbors (50)
Gene Common Name Description Module membership
PA0152 pcaQ transcriptional regulator PcaQ (NCBI) 351, 536
PA0253 PA0253 probable transcriptional regulator (NCBI) 181, 351
PA0350 folA dihydrofolate reductase (NCBI) 58, 351
PA0358 PA0358 hypothetical protein (NCBI) 181, 255
PA0378 mtgA monofunctional biosynthetic peptidoglycan transglycosylase (NCBI) 181, 438
PA0385 PA0385 hypothetical protein (NCBI) 170, 181
PA0463 creB two-component response regulator CreB (NCBI) 58, 351
PA0464 creC two-component sensor CreC (NCBI) 351, 507
PA0582 folB dihydroneopterin aldolase (NCBI) 114, 181
PA1189 PA1189 hypothetical protein (NCBI) 20, 181
PA1332 PA1332 hypothetical protein (NCBI) 108, 351
PA1375 pdxB erythronate-4-phosphate dehydrogenase (NCBI) 351, 490
PA1439 PA1439 hypothetical protein (NCBI) 181, 255
PA1788 PA1788 hypothetical protein (NCBI) 181, 528
PA1840 PA1840 hypothetical protein (NCBI) 181, 384
PA1841 PA1841 hypothetical protein (NCBI) 181, 245
PA1965 PA1965 hypothetical protein (NCBI) 139, 351
PA2251 PA2251 hypothetical protein (NCBI) 181, 206
PA2252 PA2252 probable AGCS sodium/alanine/glycine symporter (NCBI) 181, 374
PA2253 ansA L-asparaginase I (NCBI) 181, 374
PA2270 PA2270 probable transcriptional regulator (NCBI) 257, 351
PA2450 PA2450 hypothetical protein (NCBI) 139, 351
PA2502 PA2502 hypothetical protein (NCBI) 135, 351
PA2503 PA2503 hypothetical protein (NCBI) 351, 490
PA2510 catR transcriptional regulator CatR (NCBI) 307, 351
PA2855 PA2855 hypothetical protein (NCBI) 230, 351
PA2865 PA2865 probable glycosylase (NCBI) 103, 181
PA2921 PA2921 probable transcriptional regulator (NCBI) 61, 351
PA3242 PA3242 lipid A biosynthesis lauroyl acyltransferase (NCBI) 39, 181
PA3388 PA3388 hypothetical protein (NCBI) 299, 351
PA3473 PA3473 hypothetical protein (NCBI) 351, 377
PA3474 PA3474 hypothetical protein (NCBI) 351, 377
PA3573 PA3573 probable major facilitator superfamily (MFS) transporter (NCBI) 181, 299
PA3606 PA3606 hypothetical protein (NCBI) 48, 181
PA3717 PA3717 probable peptidyl-prolyl cis-trans isomerase, FkbP-type (NCBI) 181, 528
PA3726 PA3726 hypothetical protein (NCBI) 181, 247
PA3949 PA3949 hypothetical protein (NCBI) 351, 544
PA4013 PA4013 hypothetical protein (NCBI) 351, 422
PA4014 PA4014 hypothetical protein (NCBI) 58, 351
PA4512 lpxO1 lipopolysaccharide biosynthetic protein LpxO1 (NCBI) 181, 255
PA4634 PA4634 hypothetical protein (NCBI) 299, 351
PA4789 PA4789 hypothetical protein (NCBI) 229, 351
PA4790 PA4790 hypothetical protein (NCBI) 229, 351
PA4851 PA4851 hypothetical protein (NCBI) 181, 255
PA4930 alr biosynthetic alanine racemase (NCBI) 181, 255
PA4960 PA4960 probable phosphoserine phosphatase (NCBI) 114, 181
PA5127 PA5127 probable rRNA methylase (NCBI) 181, 528
PA5150 PA5150 probable short-chain dehydrogenase (NCBI) 190, 351
PA5151 PA5151 hypothetical protein (NCBI) 190, 351
PA5256 dsbH disulfide bond formation protein (NCBI) 181, 335
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 PA0253
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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