Organism : Pseudomonas aeruginosa | Module List :
PA2220

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 PA2220
(Mouseover regulator name to see its description)

PA2220 is regulated by 41 influences and regulates 8 modules.
Regulators for PA2220 (41)
Regulator Module Operator
PA0167 303 tf
PA0207 303 tf
PA1109 303 tf
PA1196 303 tf
PA1351 303 tf
PA1630 303 tf
PA1850 303 tf
PA2050 303 tf
PA2100 303 tf
PA2220 303 tf
PA2227 303 tf
PA2736 303 tf
PA3045 303 tf
PA3133 303 tf
PA3249 303 tf
PA3508 303 tf
PA4806 303 tf
PA5344 303 tf
PA0207 324 tf
PA0272 324 tf
PA0393 324 tf
PA0477 324 tf
PA0701 324 tf
PA1067 324 tf
PA1351 324 tf
PA1380 324 tf
PA1520 324 tf
PA1630 324 tf
PA2096 324 tf
PA2100 324 tf
PA2206 324 tf
PA2220 324 tf
PA2227 324 tf
PA2359 324 tf
PA2547 324 tf
PA3045 324 tf
PA3067 324 tf
PA3322 324 tf
PA3815 324 tf
PA4074 324 tf
PA4806 324 tf

Warning: PA2220 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
3432 3.50e-15 AatatcCaTTTtcAAcAttcAacT
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3433 6.30e-04 ataTGATttttttttaTtAaT..T
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3474 7.90e-04 aATGaAtATtcgGcTATgct
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3475 1.30e+00 CAACaAg.ATC
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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 PA2220

PA2220 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 PA2220

PA2220 has total of 43 gene neighbors in modules 303, 324
Gene neighbors (43)
Gene Common Name Description Module membership
PA0188 PA0188 hypothetical protein (NCBI) 324, 326
PA0204 PA0204 probable permease of ABC transporter (NCBI) 324, 355
PA0205 PA0205 probable permease of ABC transporter (NCBI) 324, 355
PA0251 PA0251 hypothetical protein (NCBI) 324, 445
PA0445 PA0445 probable transposase (NCBI) 157, 324
PA0497 PA0497 hypothetical protein (NCBI) 231, 324
PA0498 PA0498 hypothetical protein (NCBI) 231, 324
PA0689 PA0689 hypothetical protein (NCBI) 25, 324
PA0977 PA0977 hypothetical protein (NCBI) 324, 445
PA1382 PA1382 probable type II secretion system protein (NCBI) 303, 385
PA1387 PA1387 hypothetical protein (NCBI) 324, 385
PA1388 PA1388 hypothetical protein (NCBI) 324, 385
PA1389 PA1389 probable glycosyl transferase (NCBI) 324, 385
PA1390 PA1390 probable glycosyl transferase (NCBI) 254, 324
PA1391 PA1391 probable glycosyl transferase (NCBI) 254, 324
PA1392 PA1392 hypothetical protein (NCBI) 254, 324
PA1629 PA1629 probable enoyl-CoA hydratase/isomerase (NCBI) 61, 303
PA1630 PA1630 probable transcriptional regulator (NCBI) 61, 303
PA1631 PA1631 probable acyl-CoA dehydrogenase (NCBI) 61, 303
PA1935 PA1935 hypothetical protein (NCBI) 324, 445
PA2103 PA2103 probable molybdopterin biosynthesis protein MoeB (NCBI) 80, 303
PA2104 PA2104 probable cysteine synthase (NCBI) 80, 303
PA2105 PA2105 probable acetyltransferase (NCBI) 80, 303
PA2106 PA2106 hypothetical protein (NCBI) 80, 303
PA2183 PA2183 hypothetical protein (NCBI) 324, 521
PA2188 PA2188 probable alcohol dehydrogenase (Zn-dependent) (NCBI) 324, 534
PA2192 PA2192 hypothetical protein (NCBI) 324, 521
PA2219 opdE membrane protein OpdE (NCBI) 303, 324
PA2220 PA2220 probable transcriptional regulator (NCBI) 303, 324
PA2221 PA2221 hypothetical protein (NCBI) 324, 526
PA2818 arr aminoglycoside response regulator (NCBI) 31, 324
PA3065 PA3065 hypothetical protein (NCBI) 324, 438
PA3066 PA3066 hypothetical protein (NCBI) 324, 438
PA3067 PA3067 probable transcriptional regulator (NCBI) 324, 438
PA3504 PA3504 probable aldehyde dehydrogenase (NCBI) 254, 303
PA3505 PA3505 hypothetical protein (NCBI) 80, 303
PA3506 PA3506 hypothetical protein (NCBI) 254, 303
PA3510 PA3510 hypothetical protein (NCBI) 254, 303
PA3511 PA3511 probable short-chain dehydrogenase (NCBI) 80, 303
PA3512 PA3512 probable permease of ABC transporter (NCBI) 254, 303
PA3513 PA3513 hypothetical protein (NCBI) 80, 303
PA3514 PA3514 probable ATP-binding component of ABC transporter (NCBI) 80, 303
PA5088 PA5088 hypothetical protein (NCBI) 231, 324
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 PA2220
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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