Organism : Pseudomonas aeruginosa | Module List :
PA4996 rfaE

LPS biosynthesis protein RfaE (NCBI)

CircVis
Functional Annotations (8)
Function System
ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase cog/ cog
carbohydrate metabolic process go/ biological_process
biosynthetic process go/ biological_process
phosphotransferase activity, alcohol group as acceptor go/ molecular_function
nucleotidyltransferase activity go/ molecular_function
Lipopolysaccharide biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
cyt_tran_rel tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4996
(Mouseover regulator name to see its description)

PA4996 is regulated by 46 influences and regulates 0 modules.
Regulators for PA4996 rfaE (46)
Regulator Module Operator
PA0236 544 tf
PA1397 544 tf
PA1663 544 tf
PA1853 544 tf
PA2076 544 tf
PA2877 544 tf
PA3002 544 tf
PA3574 544 tf
PA3604 544 tf
PA3804 544 tf
PA4052 544 tf
PA4057 544 tf
PA4275 544 tf
PA4451 544 tf
PA4703 544 tf
PA4745 544 tf
PA4890 544 tf
PA5344 544 tf
PA0376 8 tf
PA0393 8 tf
PA0424 8 tf
PA0601 8 tf
PA1290 8 tf
PA1359 8 tf
PA1455 8 tf
PA1619 8 tf
PA2259 8 tf
PA2534 8 tf
PA2692 8 tf
PA2713 8 tf
PA2877 8 tf
PA3027 8 tf
PA3126 8 tf
PA3215 8 tf
PA3266 8 tf
PA3341 8 tf
PA4275 8 tf
PA4363 8 tf
PA4451 8 tf
PA4547 8 tf
PA4745 8 tf
PA4764 8 tf
PA4787 8 tf
PA4890 8 tf
PA5344 8 tf
PA5438 8 tf

Warning: PA4996 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
2852 5.10e+01 ttTTC.cC
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2853 1.10e+02 gCg.tcgg.AaccTgttGATtt
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3900 1.60e+00 tgGgaAaaagggCGggcagTgta
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3901 7.60e-02 TaTAaTGCtgcgCcTttttta
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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 PA4996

PA4996 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase cog/ cog
carbohydrate metabolic process go/ biological_process
biosynthetic process go/ biological_process
phosphotransferase activity, alcohol group as acceptor go/ molecular_function
nucleotidyltransferase activity go/ molecular_function
Lipopolysaccharide biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
cyt_tran_rel tigr/ tigrfam
Module neighborhood information for PA4996

PA4996 has total of 42 gene neighbors in modules 8, 544
Gene neighbors (42)
Gene Common Name Description Module membership
PA0001 dnaA chromosomal replication initiation protein (NCBI) 8, 274
PA0422 PA0422 hypothetical protein (NCBI) 8, 9
PA0609 trpE anthranilate synthetase component I (NCBI) 8, 477
PA0649 trpG anthranilate synthase component II (NCBI) 8, 139
PA0650 trpD anthranilate phosphoribosyltransferase (NCBI) 8, 477
PA0651 trpC indole-3-glycerol-phosphate synthase (NCBI) 8, 420
PA0662 argC N-acetyl-gamma-glutamyl-phosphate reductase (NCBI) 72, 544
PA0663 PA0663 hypothetical protein (NCBI) 72, 544
PA0664 PA0664 hypothetical protein (NCBI) 72, 544
PA1014 PA1014 probable glycosyl transferase (NCBI) 8, 315
PA1294 rnd ribonuclease D (NCBI) 306, 544
PA1295 PA1295 hypothetical protein (NCBI) 59, 544
PA1475 ccmA heme exporter protein CcmA (NCBI) 249, 544
PA1476 ccmB heme exporter protein CcmB (NCBI) 249, 544
PA1477 ccmC heme exporter protein CcmC (NCBI) 249, 544
PA1644 PA1644 hypothetical protein (NCBI) 8, 143
PA1727 PA1727 hypothetical protein (NCBI) 8, 261
PA1796 folD 5,10-methylene-tetrahydrofolate dehydrogenase / cyclohydrolase (NCBI) 106, 544
PA2629 purB adenylosuccinate lyase (NCBI) 106, 544
PA2755 eco ecotin precursor (NCBI) 6, 8
PA2900 PA2900 probable outer membrane protein precursor (NCBI) 8, 72
PA2901 PA2901 hypothetical protein (NCBI) 8, 117
PA2902 PA2902 hypothetical protein (NCBI) 8, 117
PA2943 PA2943 phospho-2-dehydro-3-deoxyheptonate aldolase (NCBI) 8, 9
PA3208 PA3208 hypothetical protein (NCBI) 8, 490
PA3344 recQ ATP-dependent DNA helicase RecQ (NCBI) 478, 544
PA3574 PA3574 probable transcriptional regulator (NCBI) 143, 544
PA3701 prfB peptide chain release factor H (NCBI) 308, 544
PA3881 PA3881 hypothetical protein (NCBI) 8, 321
PA3949 PA3949 hypothetical protein (NCBI) 351, 544
PA4286 PA4286 hypothetical protein (NCBI) 8, 117
PA4548 PA4548 probable D-amino acid oxidase (NCBI) 8, 220
PA4953 motB flagellar motor protein (NCBI) 8, 286
PA4954 motA flagellar motor protein (NCBI) 8, 286
PA4996 rfaE LPS biosynthesis protein RfaE (NCBI) 8, 544
PA5066 hisI phosphoribosyl-AMP cyclohydrolase (NCBI) 8, 261
PA5067 hisE phosphoribosyl-ATP pyrophosphatase (NCBI) 8, 228
PA5142 hisH1 glutamine amidotransferase (NCBI) 198, 544
PA5143 hisB imidazoleglycerol-phosphate dehydratase (NCBI) 165, 544
PA5463 PA5463 hypothetical protein (NCBI) 276, 544
PA5515 PA5515 hypothetical protein (NCBI) 8, 251
PA5528 PA5528 hypothetical protein (NCBI) 8, 327
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 PA4996
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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