Organism : Pseudomonas aeruginosa | Module List :
PA2565

hypothetical protein (NCBI)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2565
(Mouseover regulator name to see its description)

PA2565 is regulated by 47 influences and regulates 0 modules.
Regulators for PA2565 (47)
Regulator Module Operator
PA0181 124 tf
PA0367 124 tf
PA0513 124 tf
PA0547 124 tf
PA1003 124 tf
PA1182 124 tf
PA1397 124 tf
PA1570 124 tf
PA1603 124 tf
PA1663 124 tf
PA2196 124 tf
PA2432 124 tf
PA2534 124 tf
PA2588 124 tf
PA2931 124 tf
PA3126 124 tf
PA3477 124 tf
PA3583 124 tf
PA3622 124 tf
PA4132 124 tf
PA4296 124 tf
PA4530 124 tf
PA4703 124 tf
PA4755 124 tf
PA4989 124 tf
PA5059 124 tf
PA5274 124 tf
PA5374 124 tf
PA0179 159 tf
PA0652 159 tf
PA1351 159 tf
PA1603 159 tf
PA2332 159 tf
PA2849 159 tf
PA2897 159 tf
PA3266 159 tf
PA3583 159 tf
PA3815 159 tf
PA4270 159 tf
PA4296 159 tf
PA4703 159 tf
PA5059 159 tf
PA5105 159 tf
PA5274 159 tf
PA5301 159 tf
PA5344 159 tf
PA5374 159 tf

Warning: PA2565 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
3078 5.30e+01 ttaacGGAGATatA
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3079 4.70e+01 GgttgacCTGccAGatTTggcaG
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3146 1.30e-08 aTgtcggaaAaa.gctggaaAa.a
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3147 3.50e+00 GGAtTaataC..TTtc.gtgacG
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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 PA2565

Warning: No Functional annotations were found!

Module neighborhood information for PA2565

PA2565 has total of 39 gene neighbors in modules 124, 159
Gene neighbors (39)
Gene Common Name Description Module membership
PA0122 PA0122 hypothetical protein (NCBI) 112, 124
PA0852 cbpD chitin-binding protein CbpD precursor (NCBI) 112, 124
PA1121 PA1121 hypothetical protein (NCBI) 159, 388
PA1289 PA1289 hypothetical protein (NCBI) 153, 159
PA1348 PA1348 hypothetical protein (NCBI) 159, 405
PA1869 PA1869 probable acyl carrier protein (NCBI) 112, 124
PA1871 lasA LasA protease precursor (NCBI) 124, 472
PA2030 PA2030 hypothetical protein (NCBI) 124, 176
PA2031 PA2031 hypothetical protein (NCBI) 124, 176
PA2066 PA2066 hypothetical protein (NCBI) 124, 472
PA2067 PA2067 probable hydrolase (NCBI) 124, 472
PA2068 PA2068 probable major facilitator superfamily (MFS) transporter (NCBI) 124, 472
PA2069 PA2069 probable carbamoyl transferase (NCBI) 124, 472
PA2300 chiC chitinase (NCBI) 124, 176
PA2564 PA2564 hypothetical protein (NCBI) 124, 159
PA2565 PA2565 hypothetical protein (NCBI) 124, 159
PA2566 PA2566 hypothetical protein (NCBI) 124, 159
PA2570 pa1L PA-I galactophilic lectin (NCBI) 124, 472
PA2746 PA2746 hypothetical protein (NCBI) 159, 209
PA2841 PA2841 probable enoyl-CoA hydratase/isomerase (NCBI) 159, 163
PA3326 PA3326 probable Clp-family ATP-dependent protease (NCBI) 112, 124
PA3347 PA3347 hypothetical protein (NCBI) 159, 209
PA3361 lecB fucose-binding lectin PA-IIL (NCBI) 112, 124
PA3478 rhlB rhamnosyltransferase chain B (NCBI) 112, 124
PA3479 rhlA rhamnosyltransferase chain A (NCBI) 112, 124
PA3520 PA3520 hypothetical protein (NCBI) 112, 124
PA3724 lasB elastase LasB (NCBI) 112, 124
PA3734 PA3734 hypothetical protein (NCBI) 159, 472
PA3740 PA3740 hypothetical protein (NCBI) 159, 248
PA3957 PA3957 short chain dehydrogenase (NCBI) 159, 187
PA4141 PA4141 hypothetical protein (NCBI) 112, 124
PA4294 PA4294 hypothetical protein (NCBI) 54, 159
PA4295 PA4295 hypothetical protein (NCBI) 159, 321
PA4641 PA4641 None 159, 382
PA4703 PA4703 hypothetical protein (NCBI) 159, 209
PA4781 PA4781 probable two-component response regulator (NCBI) 128, 159
PA4929 PA4929 hypothetical protein (NCBI) 159, 292
PA5191 PA5191 hypothetical protein (NCBI) 159, 551
PA5220 PA5220 hypothetical protein (NCBI) 124, 472
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 PA2565
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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