Organism : Pseudomonas aeruginosa | Module List :
PA4012

hypothetical protein (NCBI)

CircVis
Functional Annotations (3)
Function System
Uncharacterized protein, similar to the N-terminal domain of Lon protease cog/ cog
ATP-dependent peptidase activity go/ molecular_function
ATP-dependent proteolysis go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4012
(Mouseover regulator name to see its description)

PA4012 is regulated by 30 influences and regulates 0 modules.
Regulators for PA4012 (30)
Regulator Module Operator
PA0179 248 tf
PA0815 248 tf
PA1309 248 tf
PA1949 248 tf
PA2220 248 tf
PA2897 248 tf
PA4021 248 tf
PA4182 248 tf
PA4238 248 tf
PA4499 248 tf
PA4703 248 tf
PA4787 248 tf
PA5255 248 tf
PA5261 248 tf
PA5288 248 tf
PA0179 209 tf
PA0815 209 tf
PA0979 209 tf
PA2586 209 tf
PA2622 209 tf
PA2897 209 tf
PA3126 209 tf
PA4269 209 tf
PA4296 209 tf
PA4703 209 tf
PA4764 209 tf
PA5255 209 tf
PA5261 209 tf
PA5288 209 tf
PA5550 209 tf

Warning: PA4012 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
3246 8.90e+00 aTtgAtcctgttcccatGatg
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3247 1.30e+04 AccATCgGCCTGgC
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3324 1.10e-02 Ag.aTaGcCaG
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3325 2.30e+01 TgTGCCtGtcgaAGGagC.gAC
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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 PA4012

PA4012 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Uncharacterized protein, similar to the N-terminal domain of Lon protease cog/ cog
ATP-dependent peptidase activity go/ molecular_function
ATP-dependent proteolysis go/ biological_process
Module neighborhood information for PA4012

PA4012 has total of 44 gene neighbors in modules 209, 248
Gene neighbors (44)
Gene Common Name Description Module membership
PA0250 PA0250 hypothetical protein (NCBI) 248, 397
PA0312 PA0312 hypothetical protein (NCBI) 70, 248
PA0332 PA0332 hypothetical protein (NCBI) 248, 547
PA0505 PA0505 hypothetical protein (NCBI) 63, 209
PA0566 PA0566 hypothetical protein (NCBI) 209, 457
PA0954 PA0954 probable acylphosphatase (NCBI) 63, 209
PA0988 PA0988 hypothetical protein (NCBI) 209, 321
PA1287 PA1287 probable glutathione peroxidase (NCBI) 166, 209
PA1377 PA1377 hypothetical protein (NCBI) 248, 513
PA1753 PA1753 hypothetical protein (NCBI) 209, 405
PA1817 PA1817 hypothetical protein (NCBI) 63, 209
PA1946 rbsB binding protein component precursor of ABC ribose transporter (NCBI) 88, 248
PA1947 rbsA ribose transport protein RbsA (NCBI) 88, 248
PA1948 rbsC membrane protein component of ABC ribose transporter (NCBI) 88, 248
PA1949 rbsR ribose operon repressor RbsR (NCBI) 88, 248
PA1950 rbsK ribokinase (NCBI) 88, 248
PA2560 PA2560 hypothetical protein (NCBI) 151, 248
PA2582 PA2582 hypothetical protein (NCBI) 209, 541
PA2668 PA2668 hypothetical protein (NCBI) 208, 209
PA2746 PA2746 hypothetical protein (NCBI) 159, 209
PA2799 PA2799 hypothetical protein (NCBI) 209, 248
PA2864 PA2864 hypothetical protein (NCBI) 185, 209
PA2989 PA2989 hypothetical protein (NCBI) 63, 209
PA3260 PA3260 probable transcriptional regulator (NCBI) 51, 248
PA3261 PA3261 hypothetical protein (NCBI) 248, 457
PA3347 PA3347 hypothetical protein (NCBI) 159, 209
PA3354 PA3354 hypothetical protein (NCBI) 248, 457
PA3740 PA3740 hypothetical protein (NCBI) 159, 248
PA3796 PA3796 hypothetical protein (NCBI) 248, 547
PA3846 PA3846 hypothetical protein (NCBI) 63, 248
PA4012 PA4012 hypothetical protein (NCBI) 209, 248
PA4021 PA4021 probable transcriptional regulator (NCBI) 163, 248
PA4111 PA4111 hypothetical protein (NCBI) 248, 457
PA4326 PA4326 hypothetical protein (NCBI) 248, 496
PA4377 PA4377 hypothetical protein (NCBI) 209, 455
PA4573 PA4573 hypothetical protein (NCBI) 209, 243
PA4674 PA4674 hypothetical protein (NCBI) 166, 209
PA4702 PA4702 hypothetical protein (NCBI) 209, 555
PA4703 PA4703 hypothetical protein (NCBI) 159, 209
PA4780 PA4780 hypothetical protein (NCBI) 245, 248
PA4787 PA4787 probable transcriptional regulator (NCBI) 70, 248
PA4870 PA4870 hypothetical protein (NCBI) 209, 224
PA5255 algQ Alginate regulatory protein AlgQ (NCBI) 51, 248
PA5460 PA5460 hypothetical protein (NCBI) 166, 209
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 PA4012
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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