Organism : Pseudomonas aeruginosa | Module List :
PA4078

probable nonribosomal peptide synthetase (NCBI)

CircVis
Functional Annotations (9)
Function System
Non-ribosomal peptide synthetase modules and related proteins cog/ cog
L-aminoadipate-semialdehyde dehydrogenase activity go/ molecular_function
metabolic process go/ biological_process
ligase activity go/ molecular_function
phosphopantetheine binding go/ molecular_function
cellular metabolic process go/ biological_process
cofactor binding go/ molecular_function
coenzyme binding go/ molecular_function
AA-adenyl-dom tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4078
(Mouseover regulator name to see its description)

PA4078 is regulated by 54 influences and regulates 0 modules.
Regulators for PA4078 (54)
Regulator Module Operator
PA0376 88 tf
PA0436 88 tf
PA0942 88 tf
PA1949 88 tf
PA2622 88 tf
PA3124 88 tf
PA3458 88 tf
PA4853 88 tf
PA5253 88 tf
PA5255 88 tf
PA5261 88 tf
PA5288 88 tf
PA0436 176 tf
PA0491 176 tf
PA0514 176 tf
PA0828 176 tf
PA1109 176 tf
PA1125 176 tf
PA1184 176 tf
PA1599 176 tf
PA2028 176 tf
PA2047 176 tf
PA2299 176 tf
PA2359 176 tf
PA2423 176 tf
PA2551 176 tf
PA2588 176 tf
PA2846 176 tf
PA2896 176 tf
PA2957 176 tf
PA3034 176 tf
PA3433 176 tf
PA3571 176 tf
PA3622 176 tf
PA3778 176 tf
PA3864 176 tf
PA3948 176 tf
PA4132 176 tf
PA4275 176 tf
PA4296 176 tf
PA4436 176 tf
PA4499 176 tf
PA4878 176 tf
PA4914 176 tf
PA5059 176 tf
PA5105 176 tf
PA5166 176 tf
PA5239 176 tf
PA5255 176 tf
PA5324 176 tf
PA5374 176 tf
PA5428 176 tf
PA5437 176 tf
PA5511 176 tf

Warning: PA4078 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
3008 1.70e-05 aAtCcgga.AaaTTC.gccaAt
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3009 1.70e-04 AGggtTTTtCCcaGcctTcgcCgT
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3180 1.20e+01 AAaAgcaagcGatAgCcacTcta
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3181 1.90e+03 AAcAgaatctTTCga
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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 PA4078

PA4078 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Non-ribosomal peptide synthetase modules and related proteins cog/ cog
L-aminoadipate-semialdehyde dehydrogenase activity go/ molecular_function
metabolic process go/ biological_process
ligase activity go/ molecular_function
phosphopantetheine binding go/ molecular_function
cellular metabolic process go/ biological_process
cofactor binding go/ molecular_function
coenzyme binding go/ molecular_function
AA-adenyl-dom tigr/ tigrfam
Module neighborhood information for PA4078

PA4078 has total of 42 gene neighbors in modules 88, 176
Gene neighbors (42)
Gene Common Name Description Module membership
PA0269 PA0269 hypothetical protein (NCBI) 176, 258
PA0270 PA0270 hypothetical protein (NCBI) 176, 258
PA0271 PA0271 hypothetical protein (NCBI) 127, 176
PA0436 PA0436 probable transcriptional regulator (NCBI) 57, 88
PA0468 PA0468 hypothetical protein (NCBI) 127, 176
PA0962 PA0962 probable dna-binding stress protein (NCBI) 88, 238
PA1053 PA1053 hypothetical protein (NCBI) 88, 376
PA1344 PA1344 probable short-chain dehydrogenase (NCBI) 176, 258
PA1784 PA1784 hypothetical protein (NCBI) 176, 367
PA1833 PA1833 probable oxidoreductase (NCBI) 88, 405
PA1946 rbsB binding protein component precursor of ABC ribose transporter (NCBI) 88, 248
PA1947 rbsA ribose transport protein RbsA (NCBI) 88, 248
PA1948 rbsC membrane protein component of ABC ribose transporter (NCBI) 88, 248
PA1949 rbsR ribose operon repressor RbsR (NCBI) 88, 248
PA1950 rbsK ribokinase (NCBI) 88, 248
PA2030 PA2030 hypothetical protein (NCBI) 124, 176
PA2031 PA2031 hypothetical protein (NCBI) 124, 176
PA2300 chiC chitinase (NCBI) 124, 176
PA2327 PA2327 probable permease of ABC transporter (NCBI) 176, 257
PA2328 PA2328 hypothetical protein (NCBI) 176, 257
PA2329 PA2329 probable ATP-binding component of ABC transporter (NCBI) 176, 257
PA2330 PA2330 hypothetical protein (NCBI) 176, 257
PA2331 PA2331 hypothetical protein (NCBI) 176, 257
PA2448 PA2448 hypothetical protein (NCBI) 176, 472
PA2738 ihfA integration host factor subunit alpha (NCBI) 88, 513
PA2788 PA2788 probable chemotaxis transducer (NCBI) 176, 462
PA3022 PA3022 hypothetical protein (NCBI) 10, 176
PA3123 PA3123 hypothetical protein (NCBI) 176, 258
PA3259 PA3259 hypothetical protein (NCBI) 88, 457
PA3529 PA3529 probable peroxidase (NCBI) 88, 381
PA3536 PA3536 hypothetical protein (NCBI) 88, 139
PA3797 PA3797 hypothetical protein (NCBI) 3, 88
PA3844 PA3844 hypothetical protein (NCBI) 88, 190
PA4078 PA4078 probable nonribosomal peptide synthetase (NCBI) 88, 176
PA4079 PA4079 short chain dehydrogenase (NCBI) 88, 176
PA4511 PA4511 hypothetical protein (NCBI) 53, 88
PA4726 cbrB two-component response regulator CbrB (NCBI) 51, 88
PA5258 PA5258 hypothetical protein (NCBI) 88, 457
PA5305 PA5305 hypothetical protein (NCBI) 87, 88
PA5306 PA5306 hypothetical protein (NCBI) 57, 88
PA5307 PA5307 hypothetical protein (NCBI) 88, 345
PA5308 lrp leucine-responsive regulatory protein (NCBI) 88, 541
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 PA4078
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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