Organism : Pseudomonas aeruginosa | Module List :
PA4057

hypothetical protein (NCBI)

CircVis
Functional Annotations (2)
Function System
Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains cog/ cog
TIGR00244 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4057
(Mouseover regulator name to see its description)

PA4057 is regulated by 36 influences and regulates 47 modules.
Regulators for PA4057 (36)
Regulator Module Operator
PA0376 228 tf
PA0393 228 tf
PA0456 228 tf
PA0576 228 tf
PA1520 228 tf
PA2736 228 tf
PA3002 228 tf
PA3604 228 tf
PA4057 228 tf
PA4275 228 tf
PA4279 228 tf
PA4600 228 tf
PA4853 228 tf
PA5116 228 tf
PA5337 228 tf
PA5344 228 tf
PA0424 278 tf
PA0576 278 tf
PA0839 278 tf
PA1196 278 tf
PA1455 278 tf
PA1526 278 tf
PA2577 278 tf
PA2885 278 tf
PA3002 278 tf
PA3007 278 tf
PA3458 278 tf
PA3948 278 tf
PA3973 278 tf
PA4052 278 tf
PA4057 278 tf
PA4269 278 tf
PA4279 278 tf
PA4530 278 tf
PA4745 278 tf
PA5308 278 tf

Warning: PA4057 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
3284 1.80e-03 GgatgtTccGgA.tAcgcca
Loader icon
3285 9.90e+00 aCGCTGagAAaggcGAgacGaaT
Loader icon
3384 1.80e-05 A.aAaAtAccatggactgCGaAAt
Loader icon
3385 6.90e-01 atgtattgcACgTgatGaAttAaG
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 PA4057

PA4057 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains cog/ cog
TIGR00244 tigr/ tigrfam
Module neighborhood information for PA4057

PA4057 has total of 33 gene neighbors in modules 228, 278
Gene neighbors (33)
Gene Common Name Description Module membership
PA0404 PA0404 Holliday junction resolvase-like protein (NCBI) 86, 278
PA0596 PA0596 hypothetical protein (NCBI) 278, 452
PA0869 pbpG D-alanyl-D-alanine-endopeptidase (NCBI) 82, 278
PA1010 dapA dihydrodipicolinate synthase (NCBI) 186, 228
PA1821 PA1821 enoyl-CoA hydratase (NCBI) 228, 478
PA1822 fimL hypothetical protein (NCBI) 228, 478
PA2744 thrS threonyl-tRNA synthetase (NCBI) 278, 395
PA3141 wbpM nucleotide sugar epimerase/dehydratase WbpM (NCBI) 278, 488
PA3244 minD cell division inhibitor MinD (NCBI) 228, 398
PA3435 PA3435 flavodoxin (NCBI) 278, 541
PA3566 PA3566 hypothetical protein (NCBI) 225, 278
PA3567 PA3567 probable oxidoreductase (NCBI) 225, 278
PA3624 pcm protein-L-isoaspartate O-methyltransferase (NCBI) 228, 262
PA3625 surE stationary phase survival protein SurE (NCBI) 18, 228
PA3657 map methionine aminopeptidase (NCBI) 228, 278
PA3978 PA3978 hypothetical protein (NCBI) 278, 452
PA4056 ribD riboflavin-specific deaminase/reductase (NCBI) 62, 228
PA4057 PA4057 hypothetical protein (NCBI) 228, 278
PA4058 PA4058 hypothetical protein (NCBI) 228, 371
PA4059 PA4059 hypothetical protein (NCBI) 228, 371
PA4060 PA4060 hypothetical protein (NCBI) 228, 387
PA4765 omlA Outer membrane lipoprotein OmlA precursor (NCBI) 228, 251
PA4916 PA4916 hypothetical protein (NCBI) 216, 278
PA4917 PA4917 hypothetical protein (NCBI) 216, 278
PA4918 PA4918 hypothetical protein (NCBI) 216, 278
PA4919 pncB1 nicotinate phosphoribosyltransferase (NCBI) 216, 278
PA4920 nadE NAD(+) synthetase (NCBI) 216, 278
PA4943 PA4943 probable GTP-binding protein (NCBI) 278, 409
PA5067 hisE phosphoribosyl-ATP pyrophosphatase (NCBI) 8, 228
PA5276 lppL Lipopeptide LppL precursor (NCBI) 41, 228
PA5277 lysA diaminopimelate decarboxylase (NCBI) 42, 228
PA5279 PA5279 hypothetical protein (NCBI) 75, 228
PA5492 PA5492 GTP-binding protein (NCBI) 129, 278
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 PA4057
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