Organism : Pseudomonas aeruginosa | Module List :
PA1963

hypothetical protein (NCBI)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1963
(Mouseover regulator name to see its description)

PA1963 is regulated by 35 influences and regulates 0 modules.
Regulators for PA1963 (35)
Regulator Module Operator
PA0376 455 tf
PA0762 455 tf
PA0763 455 tf
PA0780 455 tf
PA1159 455 tf
PA1754 455 tf
PA2259 455 tf
PA2622 455 tf
PA2897 455 tf
PA2899 455 tf
PA3002 455 tf
PA3034 455 tf
PA3266 455 tf
PA4764 455 tf
PA5255 455 tf
PA5261 455 tf
PA5324 455 tf
PA5483 455 tf
PA0167 208 tf
PA0179 208 tf
PA0376 208 tf
PA0780 208 tf
PA1125 208 tf
PA2047 208 tf
PA2622 208 tf
PA2713 208 tf
PA2718 208 tf
PA2897 208 tf
PA2899 208 tf
PA3215 208 tf
PA3689 208 tf
PA3778 208 tf
PA4269 208 tf
PA5253 208 tf
PA5255 208 tf

Warning: PA1963 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
3244 4.70e+02 atttGcgcaTagt.ttgc.TttTt
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3245 4.40e+03 CGGCG..caGcG.tTaG.tTg.cC
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3728 3.80e-01 tT.GcaGTcTtcC.cgaT.ctgcT
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3729 5.10e+02 AAtAACAAgaA
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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 PA1963

Warning: No Functional annotations were found!

Module neighborhood information for PA1963

PA1963 has total of 44 gene neighbors in modules 208, 455
Gene neighbors (44)
Gene Common Name Description Module membership
PA0060 PA0060 hypothetical protein (NCBI) 455, 547
PA0376 rpoH sigma factor RpoH (NCBI) 51, 455
PA0473 PA0473 probable glutathione S-transferase (NCBI) 163, 208
PA0953 PA0953 probable thioredoxin (NCBI) 63, 208
PA1112 PA1112 hypothetical protein (NCBI) 84, 208
PA1122 PA1122 probable peptide deformylase (NCBI) 63, 208
PA1159 PA1159 probable cold-shock protein (NCBI) 57, 455
PA1579 PA1579 hypothetical protein (NCBI) 70, 455
PA1741 PA1741 hypothetical protein (NCBI) 41, 455
PA1749 PA1749 hypothetical protein (NCBI) 208, 455
PA1814 PA1814 hypothetical protein (NCBI) 208, 243
PA1815 rnhA ribonuclease H (NCBI) 51, 208
PA1872 PA1872 hypothetical protein (NCBI) 10, 208
PA1963 PA1963 hypothetical protein (NCBI) 208, 455
PA1968 PA1968 hypothetical protein (NCBI) 208, 432
PA2559 PA2559 hypothetical protein (NCBI) 63, 208
PA2668 PA2668 hypothetical protein (NCBI) 208, 209
PA2718 PA2718 probable transcriptional regulator (NCBI) 208, 457
PA2780 PA2780 hypothetical protein (NCBI) 70, 208
PA2781 PA2781 hypothetical protein (NCBI) 70, 208
PA2899 PA2899 probable transcriptional regulator (NCBI) 208, 457
PA2915 PA2915 hypothetical protein (NCBI) 141, 208
PA2985 PA2985 hypothetical protein (NCBI) 70, 208
PA3161 ihfB integration host factor beta subunit (NCBI) 70, 455
PA3270 PA3270 hypothetical protein (NCBI) 251, 455
PA3385 amrZ alginate and motility regulator Z (NCBI) 455, 525
PA3419 PA3419 hypothetical protein (NCBI) 208, 361
PA3618 PA3618 hypothetical protein (NCBI) 70, 455
PA3684 PA3684 hypothetical protein (NCBI) 243, 455
PA3698 PA3698 hypothetical protein (NCBI) 70, 208
PA3712 PA3712 hypothetical protein (NCBI) 208, 441
PA3962 PA3962 hypothetical protein (NCBI) 6, 455
PA4324 PA4324 hypothetical protein (NCBI) 437, 455
PA4325 PA4325 hypothetical protein (NCBI) 251, 455
PA4377 PA4377 hypothetical protein (NCBI) 209, 455
PA4378 inaA InaA protein (NCBI) 251, 455
PA4379 PA4379 hypothetical protein (NCBI) 251, 455
PA4714 PA4714 hypothetical protein (NCBI) 51, 208
PA4764 fur ferric uptake regulation protein (NCBI) 251, 455
PA5028 PA5028 hypothetical protein (NCBI) 70, 455
PA5182 PA5182 hypothetical protein (NCBI) 370, 455
PA5329 PA5329 hypothetical protein (NCBI) 70, 208
PA5348 PA5348 probable DNA-binding protein (NCBI) 70, 455
PA5378 PA5378 hypothetical protein (NCBI) 208, 361
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 PA1963
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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