Organism : Pseudomonas aeruginosa | Module List :
PA3300 fadD2

long-chain-fatty-acid--CoA ligase (NCBI)

CircVis
Functional Annotations (8)
Function System
Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II cog/ cog
long-chain fatty acid-CoA ligase activity go/ molecular_function
metabolic process go/ biological_process
short-chain fatty acid-CoA ligase activity go/ molecular_function
medium-chain fatty acid-CoA ligase activity go/ molecular_function
very long-chain fatty acid-CoA ligase activity go/ molecular_function
Fatty acid metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3300
(Mouseover regulator name to see its description)

PA3300 is regulated by 32 influences and regulates 0 modules.
Regulators for PA3300 fadD2 (32)
Regulator Module Operator
PA0191 3 tf
PA0367 3 tf
PA0393 3 tf
PA0707 3 tf
PA0791 3 tf
PA1760 3 tf
PA3458 3 tf
PA4354 3 tf
PA4547 3 tf
PA5562 3 tf
PA0564 163 tf
PA0763 163 tf
PA0780 163 tf
PA0784 163 tf
PA0815 163 tf
PA0828 163 tf
PA1760 163 tf
PA2622 163 tf
PA2718 163 tf
PA3363 163 tf
PA3622 163 tf
PA3921 163 tf
PA3973 163 tf
PA4021 163 tf
PA4703 163 tf
PA4745 163 tf
PA5261 163 tf
PA5337 163 tf
PA5380 163 tf
PA5437 163 tf
PA5483 163 tf
PA5550 163 tf

Warning: PA3300 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
2842 7.10e+02 TTTttCcg
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2843 4.30e+04 AA.GT.GTttTcCTA
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3154 2.40e-03 tgGaAAAacacgaat
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3155 2.20e+02 ATCctCcGgCAaAcCAGC
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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 PA3300

PA3300 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II cog/ cog
long-chain fatty acid-CoA ligase activity go/ molecular_function
metabolic process go/ biological_process
short-chain fatty acid-CoA ligase activity go/ molecular_function
medium-chain fatty acid-CoA ligase activity go/ molecular_function
very long-chain fatty acid-CoA ligase activity go/ molecular_function
Fatty acid metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for PA3300

PA3300 has total of 56 gene neighbors in modules 3, 163
Gene neighbors (56)
Gene Common Name Description Module membership
PA0230 pcaB 3-carboxy-cis,cis-muconate cycloisomerase (NCBI) 163, 215
PA0290 PA0290 hypothetical protein (NCBI) 163, 166
PA0344 PA0344 hypothetical protein (NCBI) 163, 355
PA0416 chpD probable transcriptional regulator (NCBI) 3, 321
PA0457 PA0457 hypothetical protein (NCBI) 3, 550
PA0458 PA0458 probable major facilitator superfamily (MFS) transporter (NCBI) 3, 443
PA0470 PA0470 probable hydroxamate-type ferrisiderophore receptor (NCBI) 163, 444
PA0473 PA0473 probable glutathione S-transferase (NCBI) 163, 208
PA0597 PA0597 probable nucleotidyl transferase (NCBI) 3, 452
PA0776 PA0776 hypothetical protein (NCBI) 163, 345
PA0803 PA0803 hypothetical protein (NCBI) 163, 382
PA0808 PA0808 hypothetical protein (NCBI) 163, 443
PA0817 PA0817 probable ring-cleaving dioxygenase (NCBI) 163, 246
PA0917 kup potassium uptake protein Kup (NCBI) 3, 499
PA1039 PA1039 hypothetical protein (NCBI) 3, 338
PA1042 PA1042 hypothetical protein (NCBI) 3, 384
PA1208 PA1208 hypothetical protein (NCBI) 3, 432
PA1473 PA1473 hypothetical protein (NCBI) 3, 522
PA1521 PA1521 probable guanine deaminase (NCBI) 163, 443
PA1524 xdhA xanthine dehydrogenase (NCBI) 153, 163
PA1650 PA1650 probable transporter (NCBI) 163, 294
PA1751 PA1751 hypothetical protein (NCBI) 70, 163
PA2544 PA2544 hypothetical protein (NCBI) 163, 382
PA2706 PA2706 hypothetical protein (NCBI) 3, 185
PA2764 PA2764 hypothetical protein (NCBI) 70, 163
PA2771 PA2771 hypothetical protein (NCBI) 163, 305
PA2778 PA2778 hypothetical protein (NCBI) 87, 163
PA2841 PA2841 probable enoyl-CoA hydratase/isomerase (NCBI) 159, 163
PA3087 PA3087 hypothetical protein (NCBI) 3, 253
PA3138 uvrB excinuclease ABC subunit B (NCBI) 3, 87
PA3300 fadD2 long-chain-fatty-acid--CoA ligase (NCBI) 3, 163
PA3707 wspB hypothetical protein (NCBI) 3, 388
PA3739 PA3739 probable sodium/hydrogen antiporter (NCBI) 3, 85
PA3750 PA3750 hypothetical protein (NCBI) 3, 253
PA3797 PA3797 hypothetical protein (NCBI) 3, 88
PA3851 PA3851 hypothetical protein (NCBI) 163, 203
PA3852 PA3852 hypothetical protein (NCBI) 163, 203
PA3971 PA3971 hypothetical protein (NCBI) 163, 546
PA3972 PA3972 probable acyl-CoA dehydrogenase (NCBI) 163, 546
PA3973 PA3973 probable transcriptional regulator (NCBI) 163, 432
PA4016 PA4016 hypothetical protein (NCBI) 3, 321
PA4021 PA4021 probable transcriptional regulator (NCBI) 163, 248
PA4199 PA4199 probable acyl-CoA dehydrogenase (NCBI) 3, 443
PA4200 PA4200 hypothetical protein (NCBI) 3, 203
PA4388 PA4388 hypothetical protein (NCBI) 3, 320
PA4400 PA4400 hypothetical protein (NCBI) 3, 384
PA4401 PA4401 probable glutathione S-transferase (NCBI) 3, 384
PA4476 PA4476 hypothetical protein (NCBI) 3, 28
PA4604 PA4604 hypothetical protein (NCBI) 3, 511
PA4618 PA4618 hypothetical protein (NCBI) 3, 517
PA5014 glnE glutamate-ammonia-ligase adenylyltransferase (NCBI) 3, 62
PA5198 PA5198 LD-carboxypeptidase (NCBI) 3, 253
PA5221 PA5221 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase (NCBI) 3, 499
PA5229 PA5229 hypothetical protein (NCBI) 3, 203
PA5302 dadX catabolic alanine racemase (NCBI) 3, 517
PA5447 wbpZ glycosyltransferase WbpZ (NCBI) 3, 469
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 PA3300
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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