Organism : Pseudomonas aeruginosa | Module List :
PA1235

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 PA1235
(Mouseover regulator name to see its description)

PA1235 is regulated by 24 influences and regulates 7 modules.
Regulators for PA1235 (24)
Regulator Module Operator
PA0763 206 tf
PA1261 206 tf
PA2276 206 tf
PA2737 206 tf
PA3006 206 tf
PA4165 206 tf
PA5032 206 tf
PA5253 206 tf
PA0564 498 tf
PA0701 498 tf
PA0864 498 tf
PA1067 498 tf
PA1145 498 tf
PA1235 498 tf
PA1351 498 tf
PA2050 498 tf
PA2093 498 tf
PA3045 498 tf
PA3381 498 tf
PA3420 498 tf
PA4052 498 tf
PA4169 498 tf
PA5032 498 tf
PA5293 498 tf

Warning: PA1235 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
3240 1.60e+05 TCAAAT
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3241 4.00e+04 AAcgaATGCcAaGgcCcC
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3810 3.70e-06 GAA.gCtcCtacggAat.ggAgaa
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3811 8.70e+00 ATGCAGcagACATCGTTacgtcAA
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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 PA1235

PA1235 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 PA1235

PA1235 has total of 47 gene neighbors in modules 206, 498
Gene neighbors (47)
Gene Common Name Description Module membership
PA0014 PA0014 hypothetical protein (NCBI) 23, 498
PA0208 mdcA malonate decarboxylase alpha subunit (NCBI) 24, 206
PA0268 PA0268 probable transcriptional regulator (NCBI) 206, 258
PA0538 dsbB disulfide bond formation protein (NCBI) 220, 498
PA0539 PA0539 hypothetical protein (NCBI) 12, 498
PA0540 PA0540 hypothetical protein (NCBI) 292, 498
PA0691 PA0691 hypothetical protein (NCBI) 158, 498
PA0863 PA0863 probable oxidoreductase (NCBI) 206, 434
PA1235 PA1235 probable transcriptional regulator (NCBI) 206, 498
PA1345 PA1345 hypothetical protein (NCBI) 192, 206
PA1598 PA1598 3-methyl-2-oxobutanoate hydroxymethyltransferase (NCBI) 206, 267
PA1680 PA1680 hypothetical protein (NCBI) 206, 443
PA1879 PA1879 hypothetical protein (NCBI) 206, 434
PA2230 PA2230 hypothetical protein (NCBI) 189, 206
PA2251 PA2251 hypothetical protein (NCBI) 181, 206
PA2441 PA2441 hypothetical protein (NCBI) 33, 206
PA2457 PA2457 hypothetical protein (NCBI) 62, 206
PA2458 PA2458 hypothetical protein (NCBI) 31, 206
PA2671 PA2671 hypothetical protein (NCBI) 343, 498
PA2672 PA2672 probable type II secretion system protein (NCBI) 343, 498
PA2674 PA2674 probable type II secretion system protein (NCBI) 343, 498
PA2675 PA2675 probable type II secretion system protein (NCBI) 343, 498
PA2676 PA2676 probable type II secretion system protein (NCBI) 158, 498
PA2677 PA2677 probable type II secretion protein (NCBI) 343, 498
PA2678 PA2678 probable permease of ABC-2 transporter (NCBI) 343, 498
PA2824 PA2824 probable sensor/response regulator hybrid (NCBI) 206, 295
PA2861 ligT 2'-5' RNA ligase (NCBI) 425, 498
PA3090 PA3090 hypothetical protein (NCBI) 498, 537
PA3137 PA3137 probable major facilitator superfamily (MFS) transporter (NCBI) 434, 498
PA3223 acpD acyl carrier protein phosphodiesterase (NCBI) 206, 542
PA3454 PA3454 probable acyl-CoA thiolase (NCBI) 206, 425
PA3564 PA3564 hypothetical protein (NCBI) 206, 236
PA3619 PA3619 hypothetical protein (NCBI) 33, 498
PA3682 PA3682 hypothetical protein (NCBI) 171, 498
PA3947 PA3947 probable two-component response regulator (NCBI) 201, 498
PA4140 PA4140 hypothetical protein (NCBI) 31, 206
PA4165 PA4165 probable transcriptional regulator (NCBI) 206, 459
PA4179 PA4179 probable porin (NCBI) 206, 445
PA4517 PA4517 hypothetical protein (NCBI) 78, 206
PA4809 fdhE FdhE protein (NCBI) 31, 206
PA4864 ureD urease accessory protein (NCBI) 206, 380
PA4921 PA4921 hypothetical protein (NCBI) 206, 241
PA5033 PA5033 hypothetical protein (NCBI) 206, 218
PA5216 PA5216 probable permease of ABC iron transporter (NCBI) 98, 206
PA5238 PA5238 probable O-antigen acetylase (NCBI) 97, 498
PA5284 PA5284 hypothetical protein (NCBI) 323, 498
PA5444 PA5444 hypothetical protein (NCBI) 206, 241
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 PA1235
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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