Organism : Pseudomonas aeruginosa | Module List :
PA0275

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (4)
Function System
cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0275
(Mouseover regulator name to see its description)

PA0275 is regulated by 33 influences and regulates 9 modules.
Regulators for PA0275 (33)
Regulator Module Operator
PA0167 70 tf
PA0275 70 tf
PA0376 70 tf
PA0780 70 tf
PA0815 70 tf
PA1159 70 tf
PA2622 70 tf
PA2897 70 tf
PA2899 70 tf
PA3689 70 tf
PA4094 70 tf
PA4547 70 tf
PA4764 70 tf
PA4787 70 tf
PA4984 70 tf
PA5253 70 tf
PA5255 70 tf
PA0815 34 tf
PA0828 34 tf
PA0942 34 tf
PA1484 34 tf
PA1603 34 tf
PA2259 34 tf
PA2267 34 tf
PA2484 34 tf
PA2622 34 tf
PA2758 34 tf
PA3363 34 tf
PA3815 34 tf
PA3864 34 tf
PA4070 34 tf
PA4238 34 tf
PA5562 34 tf

Warning: PA0275 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
2900 3.00e+01 aAatCaAtATGcAta
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2901 1.60e+00 TtCataTTtaTCtaCTAaCaGacA
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2972 2.90e-06 aGcCtgcgGatcggcgcaagc
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2973 3.70e+02 CtTaTGcTtgcaCTCCcGcgagg
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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 PA0275

PA0275 is enriched for 4 functions in 3 categories.
Module neighborhood information for PA0275

PA0275 has total of 61 gene neighbors in modules 34, 70
Gene neighbors (61)
Gene Common Name Description Module membership
PA0101 PA0101 hypothetical protein (NCBI) 11, 34
PA0275 PA0275 probable transcriptional regulator (NCBI) 34, 70
PA0276 PA0276 hypothetical protein (NCBI) 30, 34
PA0312 PA0312 hypothetical protein (NCBI) 70, 248
PA0336 ygdP dinucleoside polyphosphate hydrolase (NCBI) 51, 70
PA0338 PA0338 hypothetical protein (NCBI) 34, 39
PA0529 PA0529 hypothetical protein (NCBI) 34, 536
PA0739 PA0739 probable transcriptional regulator (NCBI) 34, 61
PA0861 PA0861 hypothetical protein (NCBI) 34, 87
PA0908 PA0908 hypothetical protein (NCBI) 11, 34
PA0909 PA0909 hypothetical protein (NCBI) 11, 34
PA1036 PA1036 hypothetical protein (NCBI) 34, 457
PA1168 PA1168 hypothetical protein (NCBI) 34, 473
PA1209 PA1209 hypothetical protein (NCBI) 34, 70
PA1378 PA1378 hypothetical protein (NCBI) 70, 157
PA1579 PA1579 hypothetical protein (NCBI) 70, 455
PA1604 PA1604 hypothetical protein (NCBI) 34, 432
PA1751 PA1751 hypothetical protein (NCBI) 70, 163
PA1752 PA1752 2-dehydropantoate 2-reductase (NCBI) 70, 361
PA1890 PA1890 probable glutathione S-transferase (NCBI) 70, 338
PA2229 PA2229 hypothetical protein (NCBI) 34, 189
PA2301 PA2301 hypothetical protein (NCBI) 34, 257
PA2326 PA2326 hypothetical protein (NCBI) 34, 290
PA2337 mtlR transcriptional regulator MtlR (NCBI) 34, 494
PA2422 PA2422 hypothetical protein (NCBI) 34, 289
PA2427 PA2427 hypothetical protein (NCBI) 34, 414
PA2434 PA2434 hypothetical protein (NCBI) 34, 334
PA2436 PA2436 hypothetical protein (NCBI) 34, 257
PA2440 PA2440 hypothetical protein (NCBI) 33, 34
PA2447 PA2447 probable transcriptional regulator (NCBI) 34, 196
PA2456 PA2456 hypothetical protein (NCBI) 34, 476
PA2532 tpx thiol peroxidase (NCBI) 26, 70
PA2764 PA2764 hypothetical protein (NCBI) 70, 163
PA2780 PA2780 hypothetical protein (NCBI) 70, 208
PA2781 PA2781 hypothetical protein (NCBI) 70, 208
PA2832 tpm thiopurine methyltransferase (NCBI) 70, 220
PA2856 tesA acyl-CoA thioesterase I precursor (NCBI) 70, 117
PA2985 PA2985 hypothetical protein (NCBI) 70, 208
PA3056 PA3056 hypothetical protein (NCBI) 34, 361
PA3057 PA3057 hypothetical protein (NCBI) 34, 361
PA3161 ihfB integration host factor beta subunit (NCBI) 70, 455
PA3362 PA3362 hypothetical protein (NCBI) 30, 34
PA3363 amiR aliphatic amidase regulator (NCBI) 34, 294
PA3364 amiC aliphatic amidase expression-regulating protein (NCBI) 34, 294
PA3365 PA3365 probable chaperone (NCBI) 34, 171
PA3366 amiE aliphatic amidase (NCBI) 34, 294
PA3577 PA3577 hypothetical protein (NCBI) 70, 368
PA3618 PA3618 hypothetical protein (NCBI) 70, 455
PA3698 PA3698 hypothetical protein (NCBI) 70, 208
PA4327 PA4327 hypothetical protein (NCBI) 34, 87
PA4340 PA4340 hypothetical protein (NCBI) 70, 123
PA4507 PA4507 hypothetical protein (NCBI) 34, 44
PA4537 PA4537 hypothetical protein (NCBI) 51, 70
PA4630 PA4630 hypothetical protein (NCBI) 34, 70
PA4787 PA4787 probable transcriptional regulator (NCBI) 70, 248
PA5028 PA5028 hypothetical protein (NCBI) 70, 455
PA5329 PA5329 hypothetical protein (NCBI) 70, 208
PA5348 PA5348 probable DNA-binding protein (NCBI) 70, 455
PA5465 PA5465 hypothetical protein (NCBI) 70, 108
PA5466 PA5466 hypothetical protein (NCBI) 70, 283
PA5467 PA5467 hypothetical protein (NCBI) 70, 313
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 PA0275
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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