Organism : Pseudomonas aeruginosa | Module List :
PA0961

probable cold-shock protein (NCBI)

CircVis
Functional Annotations (3)
Function System
Cold shock proteins cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0961
(Mouseover regulator name to see its description)

PA0961 is regulated by 34 influences and regulates 63 modules.
Regulators for PA0961 (34)
Regulator Module Operator
PA0815 332 tf
PA0961 332 tf
PA2766 332 tf
PA3604 332 tf
PA3622 332 tf
PA4052 332 tf
PA4269 332 tf
PA4275 332 tf
PA4279 332 tf
PA4703 332 tf
PA4745 332 tf
PA4853 332 tf
PA4890 332 tf
PA5166 332 tf
PA5403 332 tf
PA5511 332 tf
PA5550 332 tf
PA0179 272 tf
PA0815 272 tf
PA0890 272 tf
PA0961 272 tf
PA2957 272 tf
PA3604 272 tf
PA4052 272 tf
PA4094 272 tf
PA4238 272 tf
PA4270 272 tf
PA4703 272 tf
PA4745 272 tf
PA4853 272 tf
PA4890 272 tf
PA5261 272 tf
PA5550 272 tf
PA5562 272 tf

Warning: PA0961 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
3372 9.30e+01 AtaATccCGcgccTT
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3373 4.60e+03 AtTGtg.TTTtTggAG
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3490 1.30e-02 gaagCgGcgActgTAgCaag
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3491 4.90e+01 AaAActttGCCcGtTCCGcGC
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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 PA0961

PA0961 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Cold shock proteins cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA0961

PA0961 has total of 30 gene neighbors in modules 272, 332
Gene neighbors (30)
Gene Common Name Description Module membership
PA0381 thiG thiazole synthase (NCBI) 114, 272
PA0406 PA0406 hypothetical protein (NCBI) 86, 332
PA0607 rpe ribulose-phosphate 3-epimerase (NCBI) 271, 332
PA0608 gph probable phosphoglycolate phosphatase (NCBI) 332, 451
PA0654 speD S-adenosylmethionine decarboxylase proenzyme (NCBI) 272, 308
PA0944 purN phosphoribosylglycinamide formyltransferase (NCBI) 272, 520
PA0945 purM phosphoribosylaminoimidazole synthetase (NCBI) 272, 308
PA0961 PA0961 probable cold-shock protein (NCBI) 272, 332
PA3116 PA3116 aspartate-semialdehyde dehydrogenase (NCBI) 247, 332
PA3308 hepA ATP-dependent helicase HepA (NCBI) 90, 272
PA3903 prfC peptide chain release factor 3 (NCBI) 90, 272
PA4004 PA4004 hypothetical protein (NCBI) 332, 440
PA4627 PA4627 hypothetical protein (NCBI) 332, 520
PA4636 PA4636 hypothetical protein (NCBI) 247, 332
PA4666 hemA glutamyl-tRNA reductase (NCBI) 111, 332
PA4671 PA4671 50S ribosomal protein L25 (NCBI) 272, 510
PA4672 PA4672 peptidyl-tRNA hydrolase (NCBI) 272, 510
PA4673 PA4673 hypothetical protein (NCBI) 272, 510
PA4888 PA4888 hypothetical protein (NCBI) 106, 332
PA4889 PA4889 probable oxidoreductase (NCBI) 106, 332
PA4890 PA4890 hypothetical protein (NCBI) 106, 332
PA5005 PA5005 probable carbamoyl transferase (NCBI) 174, 332
PA5129 grx glutaredoxin (NCBI) 272, 332
PA5192 pckA phosphoenolpyruvate carboxykinase (NCBI) 90, 272
PA5335 PA5335 hypothetical protein (NCBI) 332, 440
PA5357 PA5357 hypothetical protein (NCBI) 332, 374
PA5358 ubiA 4-hydroxybenzoate octaprenyltransferase (NCBI) 143, 332
PA5479 gltP proton-glutamate symporter (NCBI) 269, 272
PA5511 PA5511 probable two-component response regulator (NCBI) 332, 374
PA5513 poxA hypothetical protein (NCBI) 332, 374
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 PA0961
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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