Organism : Pseudomonas aeruginosa | Module List :
PA0154 pcaG

protocatechuate 3,4-dioxygenase, alpha subunit (NCBI)

CircVis
Functional Annotations (10)
Function System
Protocatechuate 3,4-dioxygenase beta subunit cog/ cog
ferric iron binding go/ molecular_function
protocatechuate 3,4-dioxygenase activity go/ molecular_function
aromatic compound catabolic process go/ biological_process
Benzoate degradation kegg/ kegg pathway
Polycyclic aromatic hydrocarbon degradation kegg/ kegg pathway
Aminobenzoate degradation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
protocat_alph tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0154
(Mouseover regulator name to see its description)

PA0154 is regulated by 28 influences and regulates 0 modules.
Regulators for PA0154 pcaG (28)
Regulator Module Operator
PA0152 536 tf
PA0477 536 tf
PA1264 536 tf
PA1374 536 tf
PA2838 536 tf
PA3398 536 tf
PA3420 536 tf
PA3433 536 tf
PA3757 536 tf
PA4080 536 tf
PA4184 536 tf
PA4902 536 tf
PA5293 536 tf
PA5382 536 tf
PA0533 196 tf
PA1738 196 tf
PA1945 196 tf
PA2432 196 tf
PA2447 196 tf
PA2469 196 tf
PA2489 196 tf
PA3094 196 tf
PA3124 196 tf
PA3776 196 tf
PA3778 196 tf
PA4581 196 tf
PA5029 196 tf
PA5431 196 tf

Warning: PA0154 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
3220 1.30e-15 TgaaTatatcgaaaAtCatgtAga
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3221 8.00e-07 tTt.AGGttAattGgCata.gctg
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3884 1.80e-13 A.agAaActATc.gcttcA.t.AT
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3885 6.30e-05 aAaaa.aAgAACagg
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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 PA0154

PA0154 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Protocatechuate 3,4-dioxygenase beta subunit cog/ cog
ferric iron binding go/ molecular_function
protocatechuate 3,4-dioxygenase activity go/ molecular_function
aromatic compound catabolic process go/ biological_process
Benzoate degradation kegg/ kegg pathway
Polycyclic aromatic hydrocarbon degradation kegg/ kegg pathway
Aminobenzoate degradation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
protocat_alph tigr/ tigrfam
Module neighborhood information for PA0154

PA0154 has total of 54 gene neighbors in modules 196, 536
Gene neighbors (54)
Gene Common Name Description Module membership
PA0152 pcaQ transcriptional regulator PcaQ (NCBI) 351, 536
PA0153 pcaH protocatechuate 3,4-dioxygenase, beta subunit (NCBI) 292, 536
PA0154 pcaG protocatechuate 3,4-dioxygenase, alpha subunit (NCBI) 196, 536
PA0181 PA0181 probable transcriptional regulator (NCBI) 196, 373
PA0182 PA0182 probable short-chain dehydrogenase (NCBI) 196, 313
PA0239 PA0239 hypothetical protein (NCBI) 266, 536
PA0247 pobA 4-hydroxybenzoate 3-monooxygenase (NCBI) 471, 536
PA0477 PA0477 probable transcriptional regulator (NCBI) 536, 542
PA0529 PA0529 hypothetical protein (NCBI) 34, 536
PA0530 PA0530 probable class III pyridoxal phosphate-dependent aminotransferase (NCBI) 536, 550
PA0531 PA0531 probable glutamine amidotransferase (NCBI) 23, 536
PA0575 PA0575 hypothetical protein (NCBI) 196, 483
PA1264 PA1264 probable transcriptional regulator (NCBI) 192, 536
PA1265 PA1265 hypothetical protein (NCBI) 333, 536
PA1531 PA1531 hypothetical protein (NCBI) 196, 432
PA1738 PA1738 probable transcriptional regulator (NCBI) 138, 196
PA1993 PA1993 hypothetical protein (NCBI) 196, 236
PA2269 PA2269 hypothetical protein (NCBI) 196, 326
PA2271 PA2271 probable acetyltransferase (NCBI) 196, 494
PA2344 mtlZ fructokinase (NCBI) 196, 307
PA2390 PA2390 probable ATP-binding/permease fusion ABC transporter (NCBI) 196, 414
PA2391 opmQ probable outer membrane protein precursor (NCBI) 196, 414
PA2432 PA2432 probable transcriptional regulator (NCBI) 196, 346
PA2447 PA2447 probable transcriptional regulator (NCBI) 34, 196
PA2496 PA2496 hypothetical protein (NCBI) 196, 519
PA2523 PA2523 probable two-component response regulator (NCBI) 196, 418
PA2525 PA2525 probable outer membrane protein precursor (NCBI) 104, 196
PA2526 PA2526 probable Resistance-Nodulation-Cell Division (RND) efflux transporter (NCBI) 196, 418
PA2527 PA2527 probable Resistance-Nodulation-Cell Division (RND) efflux transporter (NCBI) 196, 418
PA3124 PA3124 probable transcriptional regulator (NCBI) 196, 320
PA3125 PA3125 hypothetical protein (NCBI) 196, 497
PA3304 PA3304 hypothetical protein (NCBI) 196, 321
PA3312 PA3312 probable 3-hydroxyisobutyrate dehydrogenase (NCBI) 196, 438
PA3398 PA3398 probable transcriptional regulator (NCBI) 536, 542
PA3433 PA3433 probable transcriptional regulator (NCBI) 61, 536
PA3561 fruK 1-phosphofructokinase (NCBI) 236, 536
PA3562 PA3562 probable phosphotransferase system enzyme I (NCBI) 236, 536
PA4081 cupB6 fimbrial subunit CupB6 (NCBI) 235, 536
PA4146 PA4146 hypothetical protein (NCBI) 175, 536
PA4184 PA4184 probable transcriptional regulator (NCBI) 61, 536
PA4186 PA4186 hypothetical protein (NCBI) 125, 196
PA4398 PA4398 probable two-component sensor (NCBI) 196, 253
PA4716 PA4716 hypothetical protein (NCBI) 196, 245
PA4898 PA4898 probable porin (NCBI) 536, 538
PA4902 PA4902 probable transcriptional regulator (NCBI) 536, 538
PA4980 PA4980 probable enoyl-CoA hydratase/isomerase (NCBI) 125, 536
PA5029 PA5029 probable transcriptional regulator (NCBI) 58, 196
PA5030 PA5030 probable major facilitator superfamily (MFS) transporter (NCBI) 101, 196
PA5103 PA5103 hypothetical protein (NCBI) 171, 196
PA5126 PA5126 hypothetical protein (NCBI) 196, 321
PA5293 PA5293 probable transcriptional regulator (NCBI) 394, 536
PA5382 PA5382 probable transcriptional regulator (NCBI) 30, 536
PA5383 PA5383 hypothetical protein (NCBI) 30, 536
PA5388 PA5388 hypothetical protein (NCBI) 236, 536
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 PA0154
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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