Organism : Pseudomonas aeruginosa | Module List :
PA3885

hypothetical protein (NCBI)

CircVis
Functional Annotations (3)
Function System
Protein tyrosine/serine phosphatase cog/ cog
dephosphorylation go/ biological_process
phosphatase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3885
(Mouseover regulator name to see its description)

PA3885 is regulated by 33 influences and regulates 0 modules.
Regulators for PA3885 (33)
Regulator Module Operator
PA0207 197 tf
PA0701 197 tf
PA1067 197 tf
PA1347 197 tf
PA1380 197 tf
PA1980 197 tf
PA2785 197 tf
PA2838 197 tf
PA3381 197 tf
PA3420 197 tf
PA3594 197 tf
PA5032 197 tf
PA5293 197 tf
PA5344 197 tf
PA0207 445 tf
PA0393 445 tf
PA0491 445 tf
PA0701 445 tf
PA0828 445 tf
PA1067 445 tf
PA1347 445 tf
PA1980 445 tf
PA2050 445 tf
PA2227 445 tf
PA2547 445 tf
PA2704 445 tf
PA2737 445 tf
PA3045 445 tf
PA3133 445 tf
PA3381 445 tf
PA3420 445 tf
PA3594 445 tf
PA4806 445 tf

Warning: PA3885 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
3222 4.30e-09 aagAACaaCAAccA
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3223 8.80e+03 CAGcgCtg.gaAGT
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3710 4.00e+01 TATcgGTGaAtAATcTGA
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3711 3.70e+02 cTGGTtGAgcGCcTgGaacatCtC
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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 PA3885

PA3885 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Protein tyrosine/serine phosphatase cog/ cog
dephosphorylation go/ biological_process
phosphatase activity go/ molecular_function
Module neighborhood information for PA3885

PA3885 has total of 41 gene neighbors in modules 197, 445
Gene neighbors (41)
Gene Common Name Description Module membership
PA0202 PA0202 probable amidase (NCBI) 197, 362
PA0203 PA0203 probable binding protein component of ABC transporter (NCBI) 197, 362
PA0234 PA0234 hypothetical protein (NCBI) 156, 197
PA0251 PA0251 hypothetical protein (NCBI) 324, 445
PA0435 PA0435 hypothetical protein (NCBI) 156, 445
PA0561 PA0561 hypothetical protein (NCBI) 157, 445
PA0977 PA0977 hypothetical protein (NCBI) 324, 445
PA1368 PA1368 hypothetical protein (NCBI) 320, 445
PA1891 PA1891 hypothetical protein (NCBI) 16, 197
PA1892 PA1892 hypothetical protein (NCBI) 197, 473
PA1893 PA1893 hypothetical protein (NCBI) 197, 473
PA1919 PA1919 probable radical-activating enzyme (NCBI) 197, 311
PA1935 PA1935 hypothetical protein (NCBI) 324, 445
PA1936 PA1936 hypothetical protein (NCBI) 295, 445
PA2036 PA2036 hypothetical protein (NCBI) 231, 445
PA2064 pcoB copper resistance protein B precursor (NCBI) 197, 407
PA2065 pcoA copper resistance protein A precursor (NCBI) 197, 407
PA2079 PA2079 probable amino acid permease (NCBI) 189, 197
PA2205 PA2205 hypothetical protein (NCBI) 31, 197
PA2650 PA2650 hypothetical protein (NCBI) 187, 197
PA2655 PA2655 hypothetical protein (NCBI) 197, 434
PA2704 PA2704 probable transcriptional regulator (NCBI) 445, 497
PA2763 PA2763 hypothetical protein (NCBI) 335, 445
PA2773 PA2773 hypothetical protein (NCBI) 229, 445
PA3324 PA3324 short chain dehydrogenase (NCBI) 197, 546
PA3501 PA3501 hypothetical protein (NCBI) 254, 445
PA3502 PA3502 hypothetical protein (NCBI) 197, 254
PA3588 PA3588 probable porin (NCBI) 197, 486
PA3868 PA3868 hypothetical protein (NCBI) 197, 445
PA3885 PA3885 hypothetical protein (NCBI) 197, 445
PA3933 PA3933 probable choline transporter (NCBI) 291, 445
PA4074 PA4074 probable transcriptional regulator (NCBI) 171, 445
PA4099 PA4099 hypothetical protein (NCBI) 197, 394
PA4179 PA4179 probable porin (NCBI) 206, 445
PA4591 PA4591 hypothetical protein (NCBI) 74, 197
PA4802 PA4802 hypothetical protein (NCBI) 337, 445
PA4806 PA4806 probable transcriptional regulator (NCBI) 445, 546
PA5265 PA5265 hypothetical protein (NCBI) 104, 197
PA5266 PA5266 hypothetical protein (NCBI) 104, 197
PA5309 PA5309 probable oxidoreductase (NCBI) 335, 445
PA5532 PA5532 hypothetical protein (NCBI) 23, 445
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 PA3885
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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