Organism : Pseudomonas aeruginosa | Module List :
PA0125

hypothetical protein (NCBI)

CircVis
Functional Annotations (7)
Function System
Predicted transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
signal transducer activity go/ molecular_function
calcium ion binding go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
signal transduction go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0125
(Mouseover regulator name to see its description)

PA0125 is regulated by 38 influences and regulates 35 modules.
Regulators for PA0125 (38)
Regulator Module Operator
PA0123 309 tf
PA0125 309 tf
PA0159 309 tf
PA0163 309 tf
PA0762 309 tf
PA1285 309 tf
PA1949 309 tf
PA2020 309 tf
PA2273 309 tf
PA2299 309 tf
PA2588 309 tf
PA3815 309 tf
PA3879 309 tf
PA3932 309 tf
PA4764 309 tf
PA5157 309 tf
PA0123 412 tf
PA0125 412 tf
PA0163 412 tf
PA0424 412 tf
PA1300 412 tf
PA1309 412 tf
PA1335 412 tf
PA1359 412 tf
PA2047 412 tf
PA2277 412 tf
PA2921 412 tf
PA3007 412 tf
PA3133 412 tf
PA3266 412 tf
PA3622 412 tf
PA3815 412 tf
PA4581 412 tf
PA4745 412 tf
PA5437 412 tf
PA5438 412 tf
PA5525 412 tf
PA5562 412 tf

Warning: PA0125 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
3444 2.10e-23 aa.t.aactaaaC.tgAGtttTTa
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3445 3.10e+00 ATcaatttGcgtTtctGtaAcata
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3648 1.30e+00 GAaGaagAAgc
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3649 1.40e+01 atatAtTGGggtAgaccaTa
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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 PA0125

PA0125 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Predicted transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
signal transducer activity go/ molecular_function
calcium ion binding go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
signal transduction go/ biological_process
Module neighborhood information for PA0125

PA0125 has total of 38 gene neighbors in modules 309, 412
Gene neighbors (38)
Gene Common Name Description Module membership
PA0124 PA0124 hypothetical protein (NCBI) 309, 412
PA0125 PA0125 hypothetical protein (NCBI) 309, 412
PA0665 PA0665 hypothetical protein (NCBI) 243, 309
PA0913 mgtE probable Mg transporter MgtE (NCBI) 412, 460
PA0923 dinP DNA polymerase IV (NCBI) 299, 412
PA1297 PA1297 probable metal transporter (NCBI) 309, 412
PA1298 PA1298 hypothetical protein (NCBI) 309, 412
PA1540 PA1540 hypothetical protein (NCBI) 344, 412
PA1541 PA1541 probable drug efflux transporter (NCBI) 344, 412
PA1773 cmaX CmaX protein (NCBI) 85, 309
PA1959 bacA bacitracin resistance protein (NCBI) 299, 412
PA2019 PA2019 RND multidrug efflux membrane fusion protein precursor (NCBI) 309, 354
PA2020 PA2020 probable transcriptional regulator (NCBI) 212, 309
PA2273 PA2273 probable transcriptional regulator (NCBI) 139, 309
PA2274 PA2274 hypothetical protein (NCBI) 152, 309
PA2299 PA2299 probable transcriptional regulator (NCBI) 118, 309
PA2528 PA2528 probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein precursor (NCBI) 255, 309
PA2748 PA2748 probable methionine aminopeptidase (NCBI) 139, 412
PA2840 PA2840 probable ATP-dependent RNA helicase (NCBI) 404, 412
PA3113 trpF N-(5'-phosphoribosyl)anthranilate isomerase (NCBI) 251, 309
PA3185 PA3185 hypothetical protein (NCBI) 139, 309
PA3386 PA3386 hypothetical protein (NCBI) 362, 412
PA3664 PA3664 hypothetical protein (NCBI) 251, 412
PA3718 PA3718 probable major facilitator superfamily (MFS) transporter (NCBI) 192, 309
PA3793 PA3793 hypothetical protein (NCBI) 139, 309
PA3814 iscS L-cysteine desulfurase (pyridoxal phosphate-dependent) (NCBI) 309, 409
PA3815 PA3815 hypothetical protein (NCBI) 309, 409
PA4205 mexG hypothetical protein (NCBI) 152, 309
PA4206 mexH probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein precursor (NCBI) 152, 309
PA4207 mexI probable Resistance-Nodulation-Cell Division (RND) efflux transporter (NCBI) 152, 309
PA4208 opmD probable outer membrane protein precursor (NCBI) 152, 309
PA4520 PA4520 probable chemotaxis transducer (NCBI) 79, 309
PA4588 gdhA glutamate dehydrogenase (NCBI) 138, 309
PA4635 PA4635 hypothetical protein (NCBI) 344, 412
PA4826 PA4826 hypothetical protein (NCBI) 412, 460
PA5437 PA5437 probable transcriptional regulator (NCBI) 299, 412
PA5470 PA5470 peptide chain release factor 2 (NCBI) 412, 460
PA5471 PA5471 hypothetical protein (NCBI) 412, 460
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 PA0125
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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