Organism : Pseudomonas aeruginosa | Module List :
PA3623

hypothetical protein (NCBI)

CircVis
Functional Annotations (4)
Function System
Membrane proteins related to metalloendopeptidases cog/ cog
metalloendopeptidase activity go/ molecular_function
proteolysis go/ biological_process
cell wall macromolecule catabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3623
(Mouseover regulator name to see its description)

PA3623 is regulated by 16 influences and regulates 0 modules.
Regulators for PA3623 (16)
Regulator Module Operator
PA0393 341 tf
PA0765 341 tf
PA1898 341 tf
PA3067 341 tf
PA3285 341 tf
PA3804 341 tf
PA4070 341 tf
PA4238 341 tf
PA4451 341 tf
PA4462 341 tf
PA4600 341 tf
PA4755 341 tf
PA5239 341 tf
PA5483 341 tf
PA5550 341 tf
PA5562 341 tf

Warning: PA3623 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
3468 5.60e+02 AaacccCgtCTTTT
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3469 2.10e+01 tAaCcgggcGgcTtCGccctG.a
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3508 1.50e+02 ctTgcCGT
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3509 3.20e+03 AAAAGTACt
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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 PA3623

PA3623 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Membrane proteins related to metalloendopeptidases cog/ cog
metalloendopeptidase activity go/ molecular_function
proteolysis go/ biological_process
cell wall macromolecule catabolic process go/ biological_process
Module neighborhood information for PA3623

PA3623 has total of 54 gene neighbors in modules 321, 341
Gene neighbors (54)
Gene Common Name Description Module membership
PA0005 lptA lysophosphatidic acid acyltransferase, LptA (NCBI) 271, 341
PA0372 PA0372 probable zinc protease (NCBI) 341, 552
PA0377 PA0377 hypothetical protein (NCBI) 212, 341
PA0416 chpD probable transcriptional regulator (NCBI) 3, 321
PA0698 PA0698 hypothetical protein (NCBI) 321, 400
PA0935 PA0935 hypothetical protein (NCBI) 253, 341
PA0967 ruvB Holliday junction DNA helicase RuvB (NCBI) 69, 341
PA0971 tolA TolA protein (NCBI) 69, 341
PA0988 PA0988 hypothetical protein (NCBI) 209, 321
PA1060 PA1060 hypothetical protein (NCBI) 321, 511
PA1407 PA1407 hypothetical protein (NCBI) 321, 451
PA1506 PA1506 hypothetical protein (NCBI) 320, 321
PA1619 PA1619 probable transcriptional regulator (NCBI) 321, 362
PA1651 PA1651 probable transporter (NCBI) 320, 321
PA1834 PA1834 hypothetical protein (NCBI) 189, 321
PA1886 polB DNA polymerase II (NCBI) 321, 483
PA2126 PA2126 hypothetical protein (NCBI) 162, 321
PA2583 PA2583 probable sensor/response regulator hybrid (NCBI) 296, 321
PA2790 PA2790 hypothetical protein (NCBI) 321, 457
PA2879 PA2879 probable transcriptional regulator (NCBI) 321, 546
PA2884 PA2884 hypothetical protein (NCBI) 321, 450
PA3140 PA3140 hypothetical protein (NCBI) 321, 401
PA3197 PA3197 hypothetical protein (NCBI) 321, 374
PA3238 PA3238 hypothetical protein (NCBI) 7, 341
PA3239 PA3239 hypothetical protein (NCBI) 7, 341
PA3304 PA3304 hypothetical protein (NCBI) 196, 321
PA3305 PA3305 hypothetical protein (NCBI) 321, 546
PA3355 PA3355 hypothetical protein (NCBI) 321, 330
PA3578 PA3578 hypothetical protein (NCBI) 224, 321
PA3612 PA3612 hypothetical protein (NCBI) 341, 493
PA3623 PA3623 hypothetical protein (NCBI) 321, 341
PA3881 PA3881 hypothetical protein (NCBI) 8, 321
PA4001 sltB1 soluble lytic transglycosylase B (NCBI) 103, 341
PA4016 PA4016 hypothetical protein (NCBI) 3, 321
PA4034 aqpZ aquaporin Z (NCBI) 30, 321
PA4094 PA4094 probable transcriptional regulator (NCBI) 61, 321
PA4295 PA4295 hypothetical protein (NCBI) 159, 321
PA4452 PA4452 hypothetical protein (NCBI) 14, 341
PA4453 PA4453 hypothetical protein (NCBI) 341, 543
PA4454 PA4454 hypothetical protein (NCBI) 4, 341
PA4510 PA4510 hypothetical protein (NCBI) 321, 537
PA4531 PA4531 hypothetical protein (NCBI) 245, 321
PA4564 PA4564 hypothetical protein (NCBI) 341, 541
PA4683 PA4683 hypothetical protein (NCBI) 321, 371
PA4693 pssA phosphatidylserine synthase (NCBI) 78, 341
PA4749 glmM phosphoglucosamine mutase (NCBI) 67, 341
PA4750 folP dihydropteroate synthase (NCBI) 67, 341
PA4839 speA arginine decarboxylase (NCBI) 78, 341
PA5086 PA5086 hypothetical protein (NCBI) 231, 321
PA5126 PA5126 hypothetical protein (NCBI) 196, 321
PA5175 cysQ CysQ protein (NCBI) 220, 321
PA5177 PA5177 probable hydrolase (NCBI) 232, 321
PA5474 PA5474 probable metalloprotease (NCBI) 321, 405
PA5477 PA5477 hypothetical protein (NCBI) 321, 355
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 PA3623
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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