Organism : Pseudomonas aeruginosa | Module List :
PA1008 bcp

bacterioferritin comigratory protein (NCBI)

CircVis
Functional Annotations (4)
Function System
Peroxiredoxin cog/ cog
antioxidant activity go/ molecular_function
oxidoreductase activity go/ molecular_function
peroxiredoxin activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1008
(Mouseover regulator name to see its description)

PA1008 is regulated by 49 influences and regulates 0 modules.
Regulators for PA1008 bcp (49)
Regulator Module Operator
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
PA0179 186 tf
PA0376 186 tf
PA0576 186 tf
PA1159 186 tf
PA1467 186 tf
PA1504 186 tf
PA1539 186 tf
PA1570 186 tf
PA1826 186 tf
PA1998 186 tf
PA3002 186 tf
PA3587 186 tf
PA3771 186 tf
PA4057 186 tf
PA4182 186 tf
PA4238 186 tf
PA4270 186 tf
PA4755 186 tf
PA4853 186 tf
PA5337 186 tf
PA5344 186 tf

Warning: PA1008 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
3200 3.90e+01 AagtgTAGcgaaaa
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3201 8.30e+00 GCTgGTCatgcgcAA
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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 PA1008

PA1008 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Peroxiredoxin cog/ cog
antioxidant activity go/ molecular_function
oxidoreductase activity go/ molecular_function
peroxiredoxin activity go/ molecular_function
Module neighborhood information for PA1008

PA1008 has total of 25 gene neighbors in modules 186, 435
Gene neighbors (25)
Gene Common Name Description Module membership
PA0576 rpoD sigma factor RpoD (NCBI) 186, 433
PA0595 ostA organic solvent tolerance protein OstA precursor (NCBI) 69, 186
PA0667 PA0667 hypothetical protein (NCBI) 263, 435
PA0964 PA0964 hypothetical protein (NCBI) 69, 186
PA1008 bcp bacterioferritin comigratory protein (NCBI) 186, 435
PA1009 PA1009 hypothetical protein (NCBI) 398, 435
PA1010 dapA dihydrodipicolinate synthase (NCBI) 186, 228
PA1011 PA1011 hypothetical protein (NCBI) 186, 435
PA1013 purC phosphoribosylaminoimidazole-succinocarboxamidesynthase (NCBI) 186, 435
PA1770 ppsA phosphoenolpyruvate synthase (NCBI) 435, 436
PA1800 tig trigger factor (NCBI) 186, 506
PA2616 trxB1 thioredoxin reductase 1 (NCBI) 390, 435
PA2991 sth soluble pyridine nucleotide transhydrogenase (NCBI) 316, 435
PA3001 PA3001 glyceraldehyde-3-phosphate dehydrogenase (NCBI) 186, 433
PA3162 rpsA 30S ribosomal protein S1 (NCBI) 69, 186
PA3440 PA3440 hypothetical protein (NCBI) 237, 435
PA4031 ppa inorganic pyrophosphatase (NCBI) 122, 186
PA4426 PA4426 hypothetical protein (NCBI) 223, 435
PA4701 PA4701 hypothetical protein (NCBI) 316, 435
PA4974 PA4974 probable outer membrane protein precursor (NCBI) 435, 540
PA5013 ilvE branched-chain amino acid aminotransferase (NCBI) 186, 223
PA5128 secB export protein SecB (NCBI) 223, 435
PA5131 pgm phosphoglyceromutase (NCBI) 91, 186
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 PA1008
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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