Organism : Pseudomonas aeruginosa | Module List :
PA4132

hypothetical protein (NCBI)

CircVis
Functional Annotations (7)
Function System
Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
biosynthetic process go/ biological_process
transferase activity, transferring nitrogenous groups go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4132
(Mouseover regulator name to see its description)

PA4132 is regulated by 25 influences and regulates 26 modules.
Regulators for PA4132 (25)
Regulator Module Operator
PA0477 250 tf
PA0876 250 tf
PA1050 250 tf
PA1663 250 tf
PA1859 250 tf
PA2196 250 tf
PA2332 250 tf
PA2469 250 tf
PA2484 250 tf
PA2588 250 tf
PA2897 250 tf
PA3321 250 tf
PA3477 250 tf
PA3587 250 tf
PA3932 250 tf
PA4132 250 tf
PA4296 250 tf
PA5085 250 tf
PA5562 250 tf
PA0179 46 tf
PA3604 46 tf
PA3622 46 tf
PA4132 46 tf
PA4493 46 tf
PA5437 46 tf

Warning: PA4132 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
2924 3.20e-04 AgaAacacgatcG.TgAggGctgT
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2925 3.00e+01 atCcTgTCGcCAtaaaCaGGcgcG
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3328 7.80e+00 aTCgacagGGttTCtcCaccgATG
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3329 5.00e+01 GAagAAAC
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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 PA4132

PA4132 is enriched for 7 functions in 3 categories.
Module neighborhood information for PA4132

PA4132 has total of 32 gene neighbors in modules 46, 250
Gene neighbors (32)
Gene Common Name Description Module membership
PA0050 PA0050 hypothetical protein (NCBI) 46, 291
PA0459 PA0459 probable ClpA/B protease ATP binding subunit (NCBI) 46, 413
PA0713 PA0713 hypothetical protein (NCBI) 46, 127
PA1123 PA1123 hypothetical protein (NCBI) 46, 127
PA1548 PA1548 hypothetical protein (NCBI) 46, 511
PA1549 PA1549 probable cation-transporting P-type ATPase (NCBI) 46, 511
PA1550 PA1550 hypothetical protein (NCBI) 46, 167
PA1551 PA1551 probable ferredoxin (NCBI) 46, 167
PA1901 phzC2 phenazine biosynthesis protein PhzC (NCBI) 250, 356
PA1902 phzD2 phenazine biosynthesis protein PhzD (NCBI) 250, 356
PA1903 phzE2 phenazine biosynthesis protein PhzE (NCBI) 250, 356
PA1904 phzF2 probable phenazine biosynthesis protein (NCBI) 250, 356
PA1905 phzG2 probable pyridoxamine 5'-phosphate oxidase (NCBI) 250, 356
PA2193 hcnA hydrogen cyanide synthase HcnA (NCBI) 250, 356
PA2194 hcnB hydrogen cyanide synthase HcnB (NCBI) 250, 356
PA2195 hcnC hydrogen cyanide synthase HcnC (NCBI) 250, 356
PA3784 PA3784 hypothetical protein (NCBI) 46, 462
PA3785 PA3785 hypothetical protein (NCBI) 46, 462
PA3791 PA3791 hypothetical protein (NCBI) 46, 462
PA3928 PA3928 hypothetical protein (NCBI) 46, 64
PA3929 cioB cyanide insensitive terminal oxidase (NCBI) 46, 64
PA3930 cioA cyanide insensitive terminal oxidase (NCBI) 46, 64
PA4129 PA4129 hypothetical protein (NCBI) 46, 250
PA4130 PA4130 probable sulfite or nitrite reductase (NCBI) 46, 250
PA4131 PA4131 probable iron-sulfur protein (NCBI) 46, 250
PA4132 PA4132 hypothetical protein (NCBI) 46, 250
PA4133 PA4133 cytochrome c oxidase subunit (cbb3-type) (NCBI) 46, 250
PA4134 PA4134 hypothetical protein (NCBI) 46, 250
PA4209 phzM probable phenazine-specific methyltransferase (NCBI) 112, 250
PA4210 phzA1 probable phenazine biosynthesis protein (NCBI) 152, 250
PA4211 phzB1 probable phenazine biosynthesis protein (NCBI) 250, 356
PA4217 phzS flavin-containing monooxygenase (NCBI) 250, 356
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 PA4132
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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