Organism : Pseudomonas aeruginosa | Module List :
PA1122

probable peptide deformylase (NCBI)

CircVis
Functional Annotations (4)
Function System
N-formylmethionyl-tRNA deformylase cog/ cog
iron ion binding go/ molecular_function
translation go/ biological_process
peptide deformylase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1122
(Mouseover regulator name to see its description)

PA1122 is regulated by 38 influences and regulates 0 modules.
Regulators for PA1122 (38)
Regulator Module Operator
PA0167 208 tf
PA0179 208 tf
PA0376 208 tf
PA0780 208 tf
PA1125 208 tf
PA2047 208 tf
PA2622 208 tf
PA2713 208 tf
PA2718 208 tf
PA2897 208 tf
PA2899 208 tf
PA3215 208 tf
PA3689 208 tf
PA3778 208 tf
PA4269 208 tf
PA5253 208 tf
PA5255 208 tf
PA0179 63 tf
PA0601 63 tf
PA0763 63 tf
PA0780 63 tf
PA0815 63 tf
PA0942 63 tf
PA1283 63 tf
PA1484 63 tf
PA2020 63 tf
PA2047 63 tf
PA2622 63 tf
PA2713 63 tf
PA2718 63 tf
PA2897 63 tf
PA3225 63 tf
PA3622 63 tf
PA4021 63 tf
PA4269 63 tf
PA4769 63 tf
PA4778 63 tf
PA5255 63 tf

Warning: PA1122 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
2958 2.30e-01 AgGcTgCGggaacgcaTtTCG
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2959 4.10e+01 gGcTtTCCttaCccG
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3244 4.70e+02 atttGcgcaTagt.ttgc.TttTt
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3245 4.40e+03 CGGCG..caGcG.tTaG.tTg.cC
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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 PA1122

PA1122 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
N-formylmethionyl-tRNA deformylase cog/ cog
iron ion binding go/ molecular_function
translation go/ biological_process
peptide deformylase activity go/ molecular_function
Module neighborhood information for PA1122

PA1122 has total of 42 gene neighbors in modules 63, 208
Gene neighbors (42)
Gene Common Name Description Module membership
PA0473 PA0473 probable glutathione S-transferase (NCBI) 163, 208
PA0505 PA0505 hypothetical protein (NCBI) 63, 209
PA0862 PA0862 hypothetical protein (NCBI) 63, 141
PA0953 PA0953 probable thioredoxin (NCBI) 63, 208
PA0954 PA0954 probable acylphosphatase (NCBI) 63, 209
PA1112 PA1112 hypothetical protein (NCBI) 84, 208
PA1122 PA1122 probable peptide deformylase (NCBI) 63, 208
PA1505 moaA2 molybdopterin biosynthetic protein A2 (NCBI) 51, 63
PA1575 PA1575 hypothetical protein (NCBI) 63, 469
PA1576 PA1576 probable 3-hydroxyisobutyrate dehydrogenase (NCBI) 63, 245
PA1729 PA1729 hypothetical protein (NCBI) 63, 475
PA1749 PA1749 hypothetical protein (NCBI) 208, 455
PA1814 PA1814 hypothetical protein (NCBI) 208, 243
PA1815 rnhA ribonuclease H (NCBI) 51, 208
PA1817 PA1817 hypothetical protein (NCBI) 63, 209
PA1872 PA1872 hypothetical protein (NCBI) 10, 208
PA1963 PA1963 hypothetical protein (NCBI) 208, 455
PA1968 PA1968 hypothetical protein (NCBI) 208, 432
PA2559 PA2559 hypothetical protein (NCBI) 63, 208
PA2668 PA2668 hypothetical protein (NCBI) 208, 209
PA2718 PA2718 probable transcriptional regulator (NCBI) 208, 457
PA2756 PA2756 hypothetical protein (NCBI) 63, 457
PA2780 PA2780 hypothetical protein (NCBI) 70, 208
PA2781 PA2781 hypothetical protein (NCBI) 70, 208
PA2897 PA2897 probable transcriptional regulator (NCBI) 63, 376
PA2899 PA2899 probable transcriptional regulator (NCBI) 208, 457
PA2915 PA2915 hypothetical protein (NCBI) 141, 208
PA2985 PA2985 hypothetical protein (NCBI) 70, 208
PA2989 PA2989 hypothetical protein (NCBI) 63, 209
PA3017 PA3017 hypothetical protein (NCBI) 63, 376
PA3306 PA3306 hypothetical protein (NCBI) 63, 376
PA3307 PA3307 hypothetical protein (NCBI) 63, 475
PA3419 PA3419 hypothetical protein (NCBI) 208, 361
PA3698 PA3698 hypothetical protein (NCBI) 70, 208
PA3712 PA3712 hypothetical protein (NCBI) 208, 441
PA3846 PA3846 hypothetical protein (NCBI) 63, 248
PA4535 PA4535 hypothetical protein (NCBI) 63, 513
PA4575 PA4575 hypothetical protein (NCBI) 63, 547
PA4657 PA4657 hypothetical protein (NCBI) 63, 328
PA4714 PA4714 hypothetical protein (NCBI) 51, 208
PA5329 PA5329 hypothetical protein (NCBI) 70, 208
PA5378 PA5378 hypothetical protein (NCBI) 208, 361
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 PA1122
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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