Organism : Pseudomonas aeruginosa | Module List :
PA3629 adhC

alcohol dehydrogenase class III (NCBI)

CircVis
Functional Annotations (16)
Function System
Zn-dependent alcohol dehydrogenases, class III cog/ cog
alcohol dehydrogenase activity, metal ion-independent go/ molecular_function
alcohol dehydrogenase activity, zinc-dependent go/ molecular_function
alcohol dehydrogenase activity, iron-dependent go/ molecular_function
zinc ion binding go/ molecular_function
S-(hydroxymethyl)glutathione dehydrogenase activity go/ molecular_function
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Fatty acid metabolism kegg/ kegg pathway
Tyrosine metabolism kegg/ kegg pathway
Chloroalkane and chloroalkene degradation kegg/ kegg pathway
Naphthalene degradation kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
adh_III_F_hyde tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3629
(Mouseover regulator name to see its description)

PA3629 is regulated by 27 influences and regulates 0 modules.
Regulators for PA3629 adhC (27)
Regulator Module Operator
PA0167 488 tf
PA0367 488 tf
PA0393 488 tf
PA1754 488 tf
PA1760 488 tf
PA2096 488 tf
PA3410 488 tf
PA3622 488 tf
PA3714 488 tf
PA3965 488 tf
PA4270 488 tf
PA5253 488 tf
PA5261 488 tf
PA5562 488 tf
PA0125 381 tf
PA0236 381 tf
PA0393 381 tf
PA2047 381 tf
PA2737 381 tf
PA3458 381 tf
PA3622 381 tf
PA3879 381 tf
PA4269 381 tf
PA4462 381 tf
PA4493 381 tf
PA5253 381 tf
PA5437 381 tf

Warning: PA3629 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
3586 1.60e+03 GaAGA.Aa
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3587 6.60e+03 TTGaTTaaTGcCTGaTTATT
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3790 1.40e+03 AAagttgcATGAAa
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3791 3.50e+02 TtT.g.aGGAa
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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 PA3629

PA3629 is enriched for 16 functions in 3 categories.
Enrichment Table (16)
Function System
Zn-dependent alcohol dehydrogenases, class III cog/ cog
alcohol dehydrogenase activity, metal ion-independent go/ molecular_function
alcohol dehydrogenase activity, zinc-dependent go/ molecular_function
alcohol dehydrogenase activity, iron-dependent go/ molecular_function
zinc ion binding go/ molecular_function
S-(hydroxymethyl)glutathione dehydrogenase activity go/ molecular_function
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Fatty acid metabolism kegg/ kegg pathway
Tyrosine metabolism kegg/ kegg pathway
Chloroalkane and chloroalkene degradation kegg/ kegg pathway
Naphthalene degradation kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
adh_III_F_hyde tigr/ tigrfam
Module neighborhood information for PA3629

PA3629 has total of 36 gene neighbors in modules 381, 488
Gene neighbors (36)
Gene Common Name Description Module membership
PA0407 gshB glutathione synthetase (NCBI) 462, 488
PA0660 PA0660 hypothetical protein (NCBI) 7, 381
PA0830 PA0830 hypothetical protein (NCBI) 191, 381
PA1754 cysB transcriptional regulator CysB (NCBI) 203, 488
PA2290 gcd glucose dehydrogenase (NCBI) 191, 381
PA2318 PA2318 hypothetical protein (NCBI) 189, 381
PA2946 PA2946 hypothetical protein (NCBI) 6, 488
PA3083 pepN aminopeptidase N (NCBI) 390, 488
PA3120 leuD isopropylmalate isomerase small subunit (NCBI) 381, 477
PA3121 leuC isopropylmalate isomerase large subunit (NCBI) 381, 477
PA3141 wbpM nucleotide sugar epimerase/dehydratase WbpM (NCBI) 278, 488
PA3529 PA3529 probable peroxidase (NCBI) 88, 381
PA3628 PA3628 probable esterase (NCBI) 381, 488
PA3629 adhC alcohol dehydrogenase class III (NCBI) 381, 488
PA3752 PA3752 hypothetical protein (NCBI) 57, 488
PA3753 PA3753 hypothetical protein (NCBI) 57, 488
PA3754 PA3754 hypothetical protein (NCBI) 57, 488
PA3792 leuA 2-isopropylmalate synthase (RefSeq) 381, 488
PA3882 PA3882 hypothetical protein (NCBI) 203, 381
PA3919 PA3919 hypothetical protein (NCBI) 141, 381
PA4015 PA4015 hypothetical protein (NCBI) 141, 488
PA4236 katA catalase (NCBI) 203, 488
PA4329 pykA pyruvate kinase (NCBI) 237, 381
PA4336 PA4336 hypothetical protein (NCBI) 381, 436
PA4661 pagL Lipid A 3-O-deacylase (NCBI) 2, 488
PA4732 pgi glucose-6-phosphate isomerase (NCBI) 381, 488
PA4751 ftsH cell division protein FtsH (NCBI) 393, 488
PA4808 selA selenocysteine synthase (NCBI) 381, 540
PA4810 fdnI nitrate-inducible formate dehydrogenase, gamma subunit (NCBI) 381, 505
PA4811 fdnH nitrate-inducible formate dehydrogenase, beta subunit (NCBI) 381, 505
PA4812 fdnG formate dehydrogenase-O (NCBI) 381, 505
PA4842 PA4842 hypothetical protein (NCBI) 2, 488
PA4936 PA4936 probable rRNA methylase (NCBI) 191, 381
PA4937 rnr exoribonuclease RNase R (NCBI) 191, 381
PA5461 PA5461 hypothetical protein (NCBI) 95, 488
PA5488 PA5488 hypothetical protein (NCBI) 378, 488
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 PA3629
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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