Organism : Pseudomonas aeruginosa | Module List :
PA2616 trxB1

thioredoxin reductase 1 (NCBI)

CircVis
Functional Annotations (7)
Function System
Thioredoxin reductase cog/ cog
thioredoxin-disulfide reductase activity go/ molecular_function
cytoplasm go/ cellular_component
electron transport go/ biological_process
removal of superoxide radicals go/ biological_process
Pyrimidine metabolism kegg/ kegg pathway
TRX_reduct tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2616
(Mouseover regulator name to see its description)

PA2616 is regulated by 49 influences and regulates 0 modules.
Regulators for PA2616 trxB1 (49)
Regulator Module Operator
PA0163 390 tf
PA0279 390 tf
PA0393 390 tf
PA0831 390 tf
PA0893 390 tf
PA1128 390 tf
PA1526 390 tf
PA2047 390 tf
PA2056 390 tf
PA2312 390 tf
PA2586 390 tf
PA3002 390 tf
PA3197 390 tf
PA3563 390 tf
PA3711 390 tf
PA4270 390 tf
PA4296 390 tf
PA4341 390 tf
PA5125 390 tf
PA5166 390 tf
PA5562 390 tf
PA0167 435 tf
PA0393 435 tf
PA0576 435 tf
PA0652 435 tf
PA0873 435 tf
PA0961 435 tf
PA1504 435 tf
PA1520 435 tf
PA1539 435 tf
PA1998 435 tf
PA2054 435 tf
PA2492 435 tf
PA2511 435 tf
PA3002 435 tf
PA3094 435 tf
PA3215 435 tf
PA3322 435 tf
PA3565 435 tf
PA3699 435 tf
PA3845 435 tf
PA3927 435 tf
PA3965 435 tf
PA4238 435 tf
PA4270 435 tf
PA4462 435 tf
PA4755 435 tf
PA5253 435 tf
PA5344 435 tf

Warning: PA2616 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
3604 4.80e-02 aaacccaTCcGg.aAagcccgcC
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3605 2.90e+01 AAAtcAgcGgCAaT
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3690 3.40e+00 GGcaAggaTA
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3691 3.00e+01 AaagcgCCGcCgag.gAacCG
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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 PA2616

PA2616 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Thioredoxin reductase cog/ cog
thioredoxin-disulfide reductase activity go/ molecular_function
cytoplasm go/ cellular_component
electron transport go/ biological_process
removal of superoxide radicals go/ biological_process
Pyrimidine metabolism kegg/ kegg pathway
TRX_reduct tigr/ tigrfam
Module neighborhood information for PA2616

PA2616 has total of 34 gene neighbors in modules 390, 435
Gene neighbors (34)
Gene Common Name Description Module membership
PA0667 PA0667 hypothetical protein (NCBI) 263, 435
PA1008 bcp bacterioferritin comigratory protein (NCBI) 186, 435
PA1009 PA1009 hypothetical protein (NCBI) 398, 435
PA1011 PA1011 hypothetical protein (NCBI) 186, 435
PA1013 purC phosphoribosylaminoimidazole-succinocarboxamidesynthase (NCBI) 186, 435
PA1119 PA1119 probable outer membrane protein precursor (NCBI) 388, 390
PA1769 PA1769 hypothetical protein (NCBI) 57, 390
PA1770 ppsA phosphoenolpyruvate synthase (NCBI) 435, 436
PA2605 PA2605 hypothetical protein (NCBI) 81, 390
PA2606 PA2606 hypothetical protein (NCBI) 81, 390
PA2607 PA2607 hypothetical protein (NCBI) 81, 390
PA2608 PA2608 hypothetical protein (NCBI) 81, 390
PA2609 PA2609 hypothetical protein (NCBI) 81, 390
PA2611 cysG siroheme synthase (NCBI) 81, 390
PA2613 PA2613 hypothetical protein (NCBI) 94, 390
PA2614 lolA outer-membrane lipoprotein carrier protein precursor (NCBI) 75, 390
PA2616 trxB1 thioredoxin reductase 1 (NCBI) 390, 435
PA2617 aat leucyl/phenylalanyl-tRNA--protein transferase (NCBI) 60, 390
PA2618 PA2618 arginyl-tRNA-protein transferase (NCBI) 388, 390
PA2632 PA2632 hypothetical protein (NCBI) 390, 464
PA2633 PA2633 hypothetical protein (NCBI) 390, 464
PA2991 sth soluble pyridine nucleotide transhydrogenase (NCBI) 316, 435
PA3083 pepN aminopeptidase N (NCBI) 390, 488
PA3172 PA3172 probable hydrolase (NCBI) 179, 390
PA3198 PA3198 hypothetical protein (NCBI) 203, 390
PA3199 PA3199 hypothetical protein (NCBI) 18, 390
PA3440 PA3440 hypothetical protein (NCBI) 237, 435
PA4426 PA4426 hypothetical protein (NCBI) 223, 435
PA4701 PA4701 hypothetical protein (NCBI) 316, 435
PA4974 PA4974 probable outer membrane protein precursor (NCBI) 435, 540
PA5017 PA5017 hypothetical protein (NCBI) 95, 390
PA5128 secB export protein SecB (NCBI) 223, 435
PA5146 PA5146 hypothetical protein (NCBI) 420, 435
PA5148 PA5148 hypothetical protein (NCBI) 435, 543
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 PA2616
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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