Organism : Pseudomonas aeruginosa | Module List :
PA1599

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1599
(Mouseover regulator name to see its description)

PA1599 is regulated by 36 influences and regulates 15 modules.
Regulators for PA1599 (36)
Regulator Module Operator
PA0233 92 tf
PA0306 92 tf
PA0491 92 tf
PA0675 92 tf
PA1261 92 tf
PA1599 92 tf
PA1980 92 tf
PA2121 92 tf
PA3381 92 tf
PA3398 92 tf
PA3433 92 tf
PA3594 92 tf
PA3714 92 tf
PA4057 92 tf
PA4169 92 tf
PA4493 92 tf
PA4989 92 tf
PA5293 92 tf
PA5403 92 tf
PA5431 92 tf
PA5562 92 tf
PA0163 359 tf
PA0816 359 tf
PA0828 359 tf
PA1223 359 tf
PA1599 359 tf
PA1945 359 tf
PA2547 359 tf
PA2838 359 tf
PA2848 359 tf
PA3133 359 tf
PA3321 359 tf
PA3594 359 tf
PA4989 359 tf
PA5032 359 tf
PA5344 359 tf

Warning: PA1599 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
3016 3.50e+01 CcCaGAACAACAA.a
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3017 3.80e+03 GaTGTgAtTAtTGC
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3542 1.50e-06 aTtaatatgaAaAtcCgaattcca
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3543 5.90e-05 Atggg.TTT.gCCtGAgcAAtgC
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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 PA1599

PA1599 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for PA1599

PA1599 has total of 41 gene neighbors in modules 92, 359
Gene neighbors (41)
Gene Common Name Description Module membership
PA0058 PA0058 hypothetical protein (NCBI) 92, 425
PA0185 PA0185 probable permease of ABC transporter (NCBI) 359, 362
PA0246 PA0246 probable major facilitator superfamily (MFS) transporter (NCBI) 92, 335
PA0334 PA0334 probable major facilitator superfamily (MFS) transporter (NCBI) 92, 377
PA0466 PA0466 hypothetical protein (NCBI) 92, 132
PA0573 PA0573 hypothetical protein (NCBI) 92, 335
PA0786 PA0786 probable transporter (NCBI) 92, 537
PA0816 PA0816 probable transcriptional regulator (NCBI) 334, 359
PA1146 PA1146 probable iron-containing alcohol dehydrogenase (NCBI) 359, 463
PA1147 PA1147 probable amino acid permease (NCBI) 25, 359
PA1223 PA1223 probable transcriptional regulator (NCBI) 235, 359
PA1224 PA1224 probable NAD(P)H dehydrogenase (NCBI) 235, 359
PA1225 PA1225 probable NAD(P)H dehydrogenase (NCBI) 92, 542
PA1282 PA1282 probable major facilitator superfamily (MFS) transporter (NCBI) 92, 192
PA1542 PA1542 hypothetical protein (NCBI) 92, 546
PA1599 PA1599 probable transcriptional regulator (NCBI) 92, 359
PA1620 PA1620 hypothetical protein (NCBI) 92, 362
PA1764 PA1764 hypothetical protein (NCBI) 92, 489
PA2077 PA2077 hypothetical protein (NCBI) 16, 92
PA2535 PA2535 probable oxidoreductase (NCBI) 68, 359
PA2576 PA2576 hypothetical protein (NCBI) 359, 461
PA2578 PA2578 probable acetyltransferase (NCBI) 359, 461
PA2673 PA2673 probable type II secretion system protein (NCBI) 343, 359
PA2910 PA2910 hypothetical protein (NCBI) 68, 92
PA2925 hisM histidine transport system permease HisM (NCBI) 235, 359
PA2926 hisP histidine transport protein HisP (NCBI) 92, 285
PA3315 PA3315 probable permease of ABC transporter (NCBI) 92, 387
PA3320 PA3320 hypothetical protein (NCBI) 235, 359
PA3372 PA3372 hypothetical protein (NCBI) 92, 302
PA3593 PA3593 probable acyl-CoA dehydrogenase (NCBI) 359, 463
PA3840 PA3840 hypothetical protein (NCBI) 92, 218
PA3926 PA3926 probable major facilitator superfamily (MFS) transporter (NCBI) 340, 359
PA4178 PA4178 hypothetical protein (NCBI) 92, 372
PA4342 PA4342 probable amidase (NCBI) 201, 359
PA4822 PA4822 hypothetical protein (NCBI) 330, 359
PA4823 PA4823 hypothetical protein (NCBI) 330, 359
PA4824 PA4824 hypothetical protein (NCBI) 330, 359
PA4857 PA4857 hypothetical protein (NCBI) 92, 330
PA5032 PA5032 probable transcriptional regulator (NCBI) 340, 359
PA5402 PA5402 hypothetical protein (NCBI) 92, 99
PA5412 PA5412 hypothetical protein (NCBI) 359, 438
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 PA1599
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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