Organism : Pseudomonas aeruginosa | Module List :
PA3997 lipB

lipoyltransferase (NCBI)

CircVis
Functional Annotations (7)
Function System
Lipoate-protein ligase B cog/ cog
catalytic activity go/ molecular_function
protein modification process go/ biological_process
lipoate biosynthetic process go/ biological_process
Lipoic acid metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
lipB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3997
(Mouseover regulator name to see its description)

PA3997 is regulated by 44 influences and regulates 0 modules.
Regulators for PA3997 lipB (44)
Regulator Module Operator
PA0116 262 tf
PA0121 262 tf
PA0576 262 tf
PA0765 262 tf
PA0893 262 tf
PA0905 262 tf
PA1359 262 tf
PA1504 262 tf
PA1539 262 tf
PA2586 262 tf
PA2849 262 tf
PA2931 262 tf
PA3002 262 tf
PA3583 262 tf
PA3804 262 tf
PA4238 262 tf
PA4270 262 tf
PA4462 262 tf
PA4530 262 tf
PA4547 262 tf
PA4755 262 tf
PA4853 262 tf
PA5059 262 tf
PA5337 262 tf
PA5483 262 tf
PA5550 262 tf
PA0393 42 tf
PA0893 42 tf
PA2020 42 tf
PA2054 42 tf
PA3002 42 tf
PA3699 42 tf
PA3965 42 tf
PA4052 42 tf
PA4057 42 tf
PA4080 42 tf
PA4182 42 tf
PA4269 42 tf
PA4270 42 tf
PA4493 42 tf
PA4755 42 tf
PA5253 42 tf
PA5324 42 tf
PA5344 42 tf

Warning: PA3997 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
2916 2.00e+03 gctTGCCggcg
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2917 6.40e+02 tc.c.GCccccttCGcggcaa
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3352 2.50e+02 GtTAgAATcccccccTtaatcCa
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3353 2.80e+03 AAGTcGT
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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 PA3997

PA3997 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Lipoate-protein ligase B cog/ cog
catalytic activity go/ molecular_function
protein modification process go/ biological_process
lipoate biosynthetic process go/ biological_process
Lipoic acid metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
lipB tigr/ tigrfam
Module neighborhood information for PA3997

PA3997 has total of 29 gene neighbors in modules 42, 262
Gene neighbors (29)
Gene Common Name Description Module membership
PA0353 ilvD dihydroxy-acid dehydratase (NCBI) 42, 420
PA1615 PA1615 probable lipase (NCBI) 42, 198
PA3301 PA3301 hypothetical protein (NCBI) 42, 263
PA3302 PA3302 hypothetical protein (NCBI) 42, 436
PA3624 pcm protein-L-isoaspartate O-methyltransferase (NCBI) 228, 262
PA3645 fabZ (3R)-hydroxymyristoyl ACP dehydratase (NCBI) 256, 262
PA3646 lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (NCBI) 259, 262
PA3648 PA3648 probable outer membrane protein precursor (NCBI) 259, 262
PA3997 lipB lipoyltransferase (NCBI) 42, 262
PA4163 PA4163 amidase (NCBI) 42, 342
PA4164 PA4164 hypothetical protein (NCBI) 42, 342
PA4176 ppiC2 peptidyl-prolyl cis-trans isomerase C2 (NCBI) 42, 342
PA4180 PA4180 hypothetical protein (NCBI) 42, 342
PA4182 PA4182 hypothetical protein (NCBI) 42, 268
PA4403 secA translocase (NCBI) 113, 262
PA4423 PA4423 hypothetical protein (NCBI) 42, 263
PA4458 PA4458 hypothetical protein (NCBI) 262, 552
PA4459 PA4459 hypothetical protein (NCBI) 262, 552
PA4460 PA4460 hypothetical protein (NCBI) 223, 262
PA4461 PA4461 probable ATP-binding component of ABC transporter (NCBI) 113, 262
PA4595 PA4595 probable ATP-binding component of ABC transporter (NCBI) 42, 238
PA4907 PA4907 probable short-chain dehydrogenase (NCBI) 42, 420
PA5214 gcvH1 glycine cleavage system protein H1 (NCBI) 42, 420
PA5224 pepP aminopeptidase P (NCBI) 42, 540
PA5277 lysA diaminopimelate decarboxylase (NCBI) 42, 228
PA5278 dapF diaminopimelate epimerase (NCBI) 42, 198
PA5281 PA5281 probable hydrolase (NCBI) 42, 253
PA5338 spoT guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (NCBI) 113, 262
PA5340 PA5340 hypothetical protein (NCBI) 42, 160
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 PA3997
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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