Organism : Pseudomonas aeruginosa | Module List :
PA1607

hypothetical protein (NCBI)

CircVis
Functional Annotations (1)
Function System
Predicted transcriptional regulators cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1607
(Mouseover regulator name to see its description)

PA1607 is regulated by 35 influences and regulates 12 modules.
Regulators for PA1607 (35)
Regulator Module Operator
PA0179 457 tf
PA0601 457 tf
PA0763 457 tf
PA0815 457 tf
PA0942 457 tf
PA1125 457 tf
PA1603 457 tf
PA1607 457 tf
PA2718 457 tf
PA2897 457 tf
PA2899 457 tf
PA3034 457 tf
PA3477 457 tf
PA3689 457 tf
PA5261 457 tf
PA5288 457 tf
PA5428 457 tf
PA0456 243 tf
PA0762 243 tf
PA0815 243 tf
PA0877 243 tf
PA0939 243 tf
PA0942 243 tf
PA1607 243 tf
PA2591 243 tf
PA2713 243 tf
PA2849 243 tf
PA2896 243 tf
PA3007 243 tf
PA3587 243 tf
PA3689 243 tf
PA3804 243 tf
PA4147 243 tf
PA5116 243 tf
PA5525 243 tf

Warning: PA1607 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
3314 1.20e-11 agtc.aTaCagaaTTgGcAAgcAc
Loader icon
3315 7.30e-09 AAAAcagacctGgaaAAcaGa
Loader icon
3730 4.30e+02 actgcCtaTTcgactA.Cc
Loader icon
3731 3.40e+02 gGaAAaaC
Loader icon
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 PA1607

PA1607 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulators cog/ cog
Module neighborhood information for PA1607

PA1607 has total of 52 gene neighbors in modules 243, 457
Gene neighbors (52)
Gene Common Name Description Module membership
PA0469 PA0469 hypothetical protein (NCBI) 376, 457
PA0566 PA0566 hypothetical protein (NCBI) 209, 457
PA0601 PA0601 probable two-component response regulator (NCBI) 53, 457
PA0665 PA0665 hypothetical protein (NCBI) 243, 309
PA0810 PA0810 probable haloacid dehalogenase (NCBI) 185, 457
PA0813 PA0813 hypothetical protein (NCBI) 243, 443
PA0814 PA0814 hypothetical protein (NCBI) 243, 334
PA0815 PA0815 probable transcriptional regulator (NCBI) 243, 443
PA0877 PA0877 probable transcriptional regulator (NCBI) 243, 526
PA0907 PA0907 hypothetical protein (NCBI) 243, 468
PA0939 PA0939 hypothetical protein (NCBI) 243, 469
PA0940 PA0940 hypothetical protein (NCBI) 243, 469
PA0941 PA0941 hypothetical protein (NCBI) 243, 469
PA0942 PA0942 probable transcriptional regulator (NCBI) 243, 469
PA1036 PA1036 hypothetical protein (NCBI) 34, 457
PA1517 PA1517 hypothetical protein (NCBI) 243, 376
PA1518 PA1518 hypothetical protein (NCBI) 243, 376
PA1558 PA1558 hypothetical protein (NCBI) 220, 457
PA1603 PA1603 probable transcriptional regulator (NCBI) 53, 457
PA1607 PA1607 hypothetical protein (NCBI) 243, 457
PA1645 PA1645 hypothetical protein (NCBI) 229, 457
PA1814 PA1814 hypothetical protein (NCBI) 208, 243
PA1995 PA1995 hypothetical protein (NCBI) 457, 469
PA2713 PA2713 hypothetical protein (NCBI) 243, 475
PA2718 PA2718 probable transcriptional regulator (NCBI) 208, 457
PA2756 PA2756 hypothetical protein (NCBI) 63, 457
PA2790 PA2790 hypothetical protein (NCBI) 321, 457
PA2849 PA2849 probable transcriptional regulator (NCBI) 79, 243
PA2894 PA2894 hypothetical protein (NCBI) 27, 457
PA2899 PA2899 probable transcriptional regulator (NCBI) 208, 457
PA3256 PA3256 probable oxidoreductase (NCBI) 405, 457
PA3259 PA3259 hypothetical protein (NCBI) 88, 457
PA3261 PA3261 hypothetical protein (NCBI) 248, 457
PA3354 PA3354 hypothetical protein (NCBI) 248, 457
PA3576 PA3576 hypothetical protein (NCBI) 2, 457
PA3587 metR transcriptional regulator MetR (NCBI) 243, 550
PA3684 PA3684 hypothetical protein (NCBI) 243, 455
PA3689 PA3689 probable transcriptional regulator (NCBI) 243, 457
PA3974 ladS LadS (NCBI) 53, 243
PA4111 PA4111 hypothetical protein (NCBI) 248, 457
PA4369 PA4369 hypothetical protein (NCBI) 452, 457
PA4573 PA4573 hypothetical protein (NCBI) 209, 243
PA4656 PA4656 hypothetical protein (NCBI) 243, 245
PA4955 PA4955 hypothetical protein (NCBI) 338, 457
PA5258 PA5258 hypothetical protein (NCBI) 88, 457
PA5275 cyaY frataxin-like protein (NCBI) 243, 245
PA5371 PA5371 hypothetical protein (NCBI) 243, 251
PA5423 PA5423 hypothetical protein (NCBI) 221, 457
PA5522 PA5522 probable glutamine synthetase (NCBI) 243, 468
PA5523 PA5523 probable aminotransferase (NCBI) 243, 468
PA5524 PA5524 probable short-chain dehydrogenase (NCBI) 243, 468
PA5525 PA5525 probable transcriptional regulator (NCBI) 243, 468
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 PA1607
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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