Organism : Pseudomonas aeruginosa | Module List :
PA3126 ibpA

heat-shock protein IbpA (NCBI)

CircVis
Functional Annotations (5)
Function System
Molecular chaperone (small heat shock protein) cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3126
(Mouseover regulator name to see its description)

PA3126 is regulated by 29 influences and regulates 24 modules.
Regulators for PA3126 ibpA (29)
Regulator Module Operator
PA0393 393 tf
PA0424 393 tf
PA0576 393 tf
PA0652 393 tf
PA0905 393 tf
PA1399 393 tf
PA2123 393 tf
PA2206 393 tf
PA2588 393 tf
PA3126 393 tf
PA3225 393 tf
PA4269 393 tf
PA5324 393 tf
PA0393 10 tf
PA1197 10 tf
PA1619 10 tf
PA1754 10 tf
PA1760 10 tf
PA2047 10 tf
PA2718 10 tf
PA2737 10 tf
PA2897 10 tf
PA3126 10 tf
PA3225 10 tf
PA3622 10 tf
PA3714 10 tf
PA5253 10 tf
PA5437 10 tf
PA5483 10 tf

Warning: PA3126 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
2856 9.60e-06 GTac.TCAaGAGacTtGAcA.cgA
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2857 2.90e-03 AacgtGtcgtcGGCgtCC.GcACG
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3610 2.10e-02 TTGAAcaGccG.aaacCGcCCCta
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3611 8.50e+03 GGTTTCCA
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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 PA3126

PA3126 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Molecular chaperone (small heat shock protein) cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for PA3126

PA3126 has total of 41 gene neighbors in modules 10, 393
Gene neighbors (41)
Gene Common Name Description Module membership
PA0067 prlC oligopeptidase A (NCBI) 293, 393
PA0393 proC pyrroline-5-carboxylate reductase (NCBI) 389, 393
PA0394 PA0394 hypothetical protein (NCBI) 393, 499
PA0779 PA0779 probable ATP-dependent protease (NCBI) 393, 509
PA1115 PA1115 hypothetical protein (NCBI) 10, 399
PA1596 htpG heat shock protein 90 (NCBI) 393, 509
PA1597 PA1597 hypothetical protein (NCBI) 393, 509
PA1623 PA1623 hypothetical protein (NCBI) 10, 368
PA1624 PA1624 hypothetical protein (NCBI) 10, 320
PA1803 lon Lon protease (NCBI) 393, 464
PA1872 PA1872 hypothetical protein (NCBI) 10, 208
PA2025 gor glutathione reductase (NCBI) 10, 205
PA2620 clpA ATP-binding protease component ClpA (NCBI) 10, 525
PA2830 htpX heat shock protein HtpX (NCBI) 393, 524
PA3010 PA3010 hypothetical protein (NCBI) 10, 316
PA3022 PA3022 hypothetical protein (NCBI) 10, 176
PA3052 PA3052 hypothetical protein (NCBI) 10, 378
PA3126 ibpA heat-shock protein IbpA (NCBI) 10, 393
PA3127 PA3127 hypothetical protein (NCBI) 10, 523
PA3128 PA3128 short chain dehydrogenase (NCBI) 10, 258
PA3224 PA3224 hypothetical protein (NCBI) 2, 10
PA3225 PA3225 probable transcriptional regulator (NCBI) 2, 10
PA3226 PA3226 probable hydrolase (NCBI) 2, 10
PA3228 PA3228 probable ATP-binding/permease fusion ABC transporter (NCBI) 2, 10
PA3786 PA3786 hypothetical protein (NCBI) 10, 203
PA4061 PA4061 probable thioredoxin (NCBI) 393, 509
PA4385 groEL chaperonin GroEL (NCBI) 393, 509
PA4386 groES co-chaperonin GroES (NCBI) 393, 509
PA4387 PA4387 hypothetical protein (NCBI) 393, 509
PA4397 panE 2-dehydropantoate 2-reductase (NCBI) 10, 443
PA4399 PA4399 hypothetical protein (NCBI) 10, 53
PA4474 PA4474 hypothetical protein (NCBI) 10, 28
PA4542 clpB ClpB protein (NCBI) 393, 509
PA4751 ftsH cell division protein FtsH (NCBI) 393, 488
PA4759 dapB dihydrodipicolinate reductase (NCBI) 393, 509
PA4760 dnaJ DnaJ protein (NCBI) 393, 509
PA4761 dnaK molecular chaperone DnaK (NCBI) 393, 509
PA4762 grpE heat shock protein GrpE (NCBI) 393, 509
PA5053 hslV ATP-dependent protease peptidase subunit (NCBI) 393, 509
PA5054 hslU ATP-dependent protease ATP-binding subunit (NCBI) 393, 509
PA5055 PA5055 hypothetical protein (NCBI) 393, 509
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 PA3126
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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