Organism : Pseudomonas aeruginosa | Module List :
PA3381

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
C_P_lyase_phnF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3381
(Mouseover regulator name to see its description)

PA3381 is regulated by 27 influences and regulates 48 modules.
Regulators for PA3381 (27)
Regulator Module Operator
PA0675 357 tf
PA0701 357 tf
PA0707 357 tf
PA1226 357 tf
PA1351 357 tf
PA1826 357 tf
PA2121 357 tf
PA2206 357 tf
PA2489 357 tf
PA2696 357 tf
PA3249 357 tf
PA3381 357 tf
PA5365 357 tf
PA5511 357 tf
PA0675 302 tf
PA0701 302 tf
PA0707 302 tf
PA0828 302 tf
PA0979 302 tf
PA1226 302 tf
PA1945 302 tf
PA2028 302 tf
PA2489 302 tf
PA2696 302 tf
PA2879 302 tf
PA3381 302 tf
PA5365 302 tf

Warning: PA3381 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
3430 3.50e-03 ctGTCaccgtagCgTCaC
Loader icon
3431 2.20e+04 TTGGCTGCAAT
Loader icon
3538 4.00e-01 atTGtcAC.aaAgCGTCAc
Loader icon
3539 4.90e+03 CcGTcGaTCAa
Loader icon
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 PA3381

PA3381 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
C_P_lyase_phnF tigr/ tigrfam
Module neighborhood information for PA3381

PA3381 has total of 28 gene neighbors in modules 302, 357
Gene neighbors (28)
Gene Common Name Description Module membership
PA1606 PA1606 hypothetical protein (NCBI) 211, 302
PA2022 PA2022 probable nucleotide sugar dehydrogenase (NCBI) 211, 302
PA2428 PA2428 hypothetical protein (NCBI) 289, 302
PA2548 PA2548 hypothetical protein (NCBI) 302, 357
PA2635 PA2635 hypothetical protein (NCBI) 302, 357
PA2804 PA2804 hypothetical protein (NCBI) 302, 357
PA2881 PA2881 probable two-component response regulator (NCBI) 89, 302
PA2882 PA2882 probable two-component sensor (NCBI) 89, 302
PA3280 oprO Pyrophosphate-specific outer membrane porin OprO precursor (NCBI) 48, 302
PA3296 phoA alkaline phosphatase (NCBI) 89, 357
PA3319 plcN non-hemolytic phospholipase C precursor (NCBI) 357, 545
PA3368 PA3368 probable acetyltransferase (NCBI) 33, 302
PA3372 PA3372 hypothetical protein (NCBI) 92, 302
PA3374 PA3374 hypothetical protein (NCBI) 89, 357
PA3375 PA3375 probable ATP-binding component of ABC transporter (NCBI) 89, 302
PA3376 PA3376 probable ATP-binding component of ABC transporter (NCBI) 89, 357
PA3377 PA3377 hypothetical protein (NCBI) 89, 357
PA3378 PA3378 hypothetical protein (NCBI) 89, 357
PA3379 PA3379 hypothetical protein (NCBI) 89, 357
PA3380 PA3380 hypothetical protein (NCBI) 302, 357
PA3381 PA3381 probable transcriptional regulator (NCBI) 302, 357
PA3382 phnE phosphonate transport protein PhnE (NCBI) 89, 357
PA3383 PA3383 binding protein component of ABC phosphonate transporter (NCBI) 302, 357
PA3384 phnC ATP-binding component of ABC phosphonate transporter (NCBI) 89, 357
PA3909 PA3909 hypothetical protein (NCBI) 89, 357
PA3910 PA3910 hypothetical protein (NCBI) 211, 302
PA4350 PA4350 hypothetical protein (NCBI) 302, 357
PA5368 pstC membrane protein component of ABC phosphate transporter (NCBI) 48, 302
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 PA3381
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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