Organism : Pseudomonas aeruginosa | Module List :
PA2802

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 PA2802
(Mouseover regulator name to see its description)

PA2802 is regulated by 35 influences and regulates 13 modules.
Regulators for PA2802 (35)
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
PA0125 139 tf
PA0611 139 tf
PA0831 139 tf
PA1359 139 tf
PA1467 139 tf
PA1607 139 tf
PA1853 139 tf
PA2047 139 tf
PA2056 139 tf
PA2115 139 tf
PA2277 139 tf
PA2484 139 tf
PA2802 139 tf
PA3266 139 tf
PA3341 139 tf
PA3604 139 tf
PA4145 139 tf
PA4764 139 tf
PA4769 139 tf
PA5356 139 tf

Warning: PA2802 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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3108 9.00e+00 aAAAAAcCgCtcag
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3109 7.40e+03 GcgTTAcCAtg
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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 PA2802

PA2802 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 PA2802

PA2802 has total of 46 gene neighbors in modules 72, 139
Gene neighbors (46)
Gene Common Name Description Module membership
PA0243 PA0243 probable transcriptional regulator (NCBI) 72, 220
PA0307 PA0307 hypothetical protein (NCBI) 72, 245
PA0351 PA0351 hypothetical protein (NCBI) 72, 220
PA0362 fdx1 ferredoxin (4Fe-4S) (NCBI) 139, 354
PA0363 coaD phosphopantetheine adenylyltransferase (NCBI) 72, 178
PA0649 trpG anthranilate synthase component II (NCBI) 8, 139
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
PA0756 PA0756 probable two-component response regulator (NCBI) 139, 283
PA0831 oruR transcriptional regulator OruR (NCBI) 58, 139
PA0868 PA0868 hypothetical protein (NCBI) 72, 220
PA1075 PA1075 hypothetical protein (NCBI) 139, 229
PA1164 PA1164 hypothetical protein (NCBI) 139, 528
PA1263 PA1263 hypothetical protein (NCBI) 9, 72
PA1357 PA1357 hypothetical protein (NCBI) 72, 220
PA1359 PA1359 probable transcriptional regulator (NCBI) 139, 173
PA1965 PA1965 hypothetical protein (NCBI) 139, 351
PA2273 PA2273 probable transcriptional regulator (NCBI) 139, 309
PA2450 PA2450 hypothetical protein (NCBI) 139, 351
PA2484 PA2484 hypothetical protein (NCBI) 139, 494
PA2568 PA2568 hypothetical protein (NCBI) 139, 229
PA2748 PA2748 probable methionine aminopeptidase (NCBI) 139, 412
PA2770 PA2770 hypothetical protein (NCBI) 139, 299
PA2798 PA2798 probable two-component response regulator (NCBI) 72, 195
PA2802 PA2802 probable transcriptional regulator (NCBI) 72, 139
PA2900 PA2900 probable outer membrane protein precursor (NCBI) 8, 72
PA2979 kdsB 3-deoxy-manno-octulosonate cytidylyltransferase (NCBI) 72, 165
PA3005 nagZ beta-hexosaminidase (NCBI) 72, 165
PA3185 PA3185 hypothetical protein (NCBI) 139, 309
PA3345 PA3345 hypothetical protein (NCBI) 139, 387
PA3453 PA3453 hypothetical protein (NCBI) 58, 72
PA3463 PA3463 hypothetical protein (NCBI) 72, 229
PA3536 PA3536 hypothetical protein (NCBI) 88, 139
PA3585 glpM membrane protein GlpM (NCBI) 72, 114
PA3627 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (NCBI) 62, 139
PA3793 PA3793 hypothetical protein (NCBI) 139, 309
PA3794 PA3794 hypothetical protein (NCBI) 139, 490
PA3854 PA3854 hypothetical protein (NCBI) 72, 117
PA4637 PA4637 hypothetical protein (NCBI) 139, 229
PA4718 PA4718 hypothetical protein (NCBI) 139, 229
PA4766 PA4766 hypothetical protein (NCBI) 44, 139
PA4767 PA4767 hypothetical protein (NCBI) 139, 251
PA5176 PA5176 hypothetical protein (NCBI) 139, 251
PA5334 rph ribonuclease PH (NCBI) 139, 232
PA5363 PA5363 hypothetical protein (NCBI) 139, 251
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 PA2802
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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