Organism : Pseudomonas aeruginosa | Module List :
PA2551

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 PA2551
(Mouseover regulator name to see its description)

PA2551 is regulated by 35 influences and regulates 8 modules.
Regulators for PA2551 (35)
Regulator Module Operator
PA0179 258 tf
PA0268 258 tf
PA0479 258 tf
PA0797 258 tf
PA1125 258 tf
PA2047 258 tf
PA2551 258 tf
PA2622 258 tf
PA2737 258 tf
PA3622 258 tf
PA3778 258 tf
PA4853 258 tf
PA4890 258 tf
PA5059 258 tf
PA5105 258 tf
PA5239 258 tf
PA5253 258 tf
PA5374 258 tf
PA5403 258 tf
PA5437 258 tf
PA5550 258 tf
PA0289 397 tf
PA0448 397 tf
PA0479 397 tf
PA0784 397 tf
PA1067 397 tf
PA1760 397 tf
PA2047 397 tf
PA2551 397 tf
PA2577 397 tf
PA3757 397 tf
PA3973 397 tf
PA4914 397 tf
PA5218 397 tf
PA5550 397 tf

Warning: PA2551 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
3344 2.60e-04 AAgaaAaAGacaGGccaAgTcTtA
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3345 4.40e-05 a..agccaAttAccAGAAA.a.Ct
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3618 1.80e-07 aAaatTaGacTggtaaaAtcTtaA
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3619 6.20e-04 CAA.AAca
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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 PA2551

PA2551 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 PA2551

PA2551 has total of 41 gene neighbors in modules 258, 397
Gene neighbors (41)
Gene Common Name Description Module membership
PA0250 PA0250 hypothetical protein (NCBI) 248, 397
PA0268 PA0268 probable transcriptional regulator (NCBI) 206, 258
PA0269 PA0269 hypothetical protein (NCBI) 176, 258
PA0270 PA0270 hypothetical protein (NCBI) 176, 258
PA0479 PA0479 probable transcriptional regulator (NCBI) 397, 523
PA0792 prpD 2-methylcitrate dehydratase (NCBI) 141, 258
PA1027 PA1027 probable aldehyde dehydrogenase (NCBI) 258, 397
PA1202 PA1202 probable hydrolase (NCBI) 258, 405
PA1203 PA1203 hypothetical protein (NCBI) 258, 338
PA1205 PA1205 hypothetical protein (NCBI) 258, 523
PA1344 PA1344 probable short-chain dehydrogenase (NCBI) 176, 258
PA1523 xdhB xanthine dehydrogenase (NCBI) 153, 397
PA1617 PA1617 probable AMP-binding enzyme (NCBI) 294, 397
PA1618 PA1618 hypothetical protein (NCBI) 397, 523
PA1672 PA1672 hypothetical protein (NCBI) 245, 397
PA2035 PA2035 acetolactate synthase II large subunit (NCBI) 397, 523
PA2550 PA2550 probable acyl-CoA dehydrogenase (NCBI) 258, 397
PA2551 PA2551 probable transcriptional regulator (NCBI) 258, 397
PA2577 PA2577 probable transcriptional regulator (NCBI) 397, 523
PA2820 PA2820 hypothetical protein (NCBI) 397, 551
PA2821 PA2821 probable glutathione S-transferase (NCBI) 397, 551
PA3123 PA3123 hypothetical protein (NCBI) 176, 258
PA3128 PA3128 short chain dehydrogenase (NCBI) 10, 258
PA3346 PA3346 probable two-component response regulator (NCBI) 258, 382
PA3427 PA3427 probable short-chain dehydrogenases (NCBI) 397, 523
PA3757 PA3757 probable transcriptional regulator (NCBI) 397, 523
PA3758 PA3758 probable N-acetylglucosamine-6-phosphate deacetylase (NCBI) 397, 523
PA3847 PA3847 hypothetical protein (NCBI) 397, 443
PA3858 PA3858 probable amino acid-binding protein (NCBI) 258, 397
PA4594 PA4594 probable ATP-binding component of ABC transporter (NCBI) 338, 397
PA4875 PA4875 hypothetical protein (NCBI) 397, 443
PA4914 PA4914 probable transcriptional regulator (NCBI) 397, 537
PA4976 aspC aspartate transaminase (NCBI) 397, 523
PA5100 hutU urocanate hydratase (NCBI) 145, 258
PA5185 PA5185 hypothetical protein (NCBI) 136, 397
PA5186 PA5186 probable iron-containing alcohol dehydrogenase (NCBI) 136, 397
PA5187 PA5187 probable acyl-CoA dehydrogenase (NCBI) 136, 397
PA5188 PA5188 probable 3-hydroxyacyl-CoA dehydrogenase (NCBI) 136, 397
PA5189 PA5189 probable transcriptional regulator (NCBI) 136, 397
PA5422 PA5422 hypothetical protein (NCBI) 397, 469
PA5546 PA5546 hypothetical protein (NCBI) 258, 405
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 PA2551
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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