Organism : Pseudomonas aeruginosa | Module List :
PA4669 ipk

4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (NCBI)

CircVis
Functional Annotations (10)
Function System
4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate synthase cog/ cog
ATP binding go/ molecular_function
terpenoid biosynthetic process go/ biological_process
phosphorylation go/ biological_process
4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity go/ molecular_function
Terpenoid backbone biosynthesis kegg/ kegg pathway
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
ispE tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4669
(Mouseover regulator name to see its description)

PA4669 is regulated by 31 influences and regulates 0 modules.
Regulators for PA4669 ipk (31)
Regulator Module Operator
PA0125 49 tf
PA0159 49 tf
PA0167 49 tf
PA0893 49 tf
PA1335 49 tf
PA3002 49 tf
PA4109 49 tf
PA4269 49 tf
PA4462 49 tf
PA4493 49 tf
PA5166 49 tf
PA0167 480 tf
PA0893 480 tf
PA0961 480 tf
PA1269 480 tf
PA1335 480 tf
PA1526 480 tf
PA1850 480 tf
PA2859 480 tf
PA3002 480 tf
PA3067 480 tf
PA3583 480 tf
PA3804 480 tf
PA4270 480 tf
PA4462 480 tf
PA4530 480 tf
PA4547 480 tf
PA4755 480 tf
PA5105 480 tf
PA5166 480 tf
PA5261 480 tf

Warning: PA4669 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
2930 1.50e+03 CgGGGAaAAc
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2931 1.80e+04 AATTGtTTACAT
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3776 2.40e+02 catgcATTtC
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3777 1.30e+04 aggCcAtCgTCcTCgaCgAC
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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 PA4669

PA4669 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate synthase cog/ cog
ATP binding go/ molecular_function
terpenoid biosynthetic process go/ biological_process
phosphorylation go/ biological_process
4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity go/ molecular_function
Terpenoid backbone biosynthesis kegg/ kegg pathway
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
ispE tigr/ tigrfam
Module neighborhood information for PA4669

PA4669 has total of 45 gene neighbors in modules 49, 480
Gene neighbors (45)
Gene Common Name Description Module membership
PA0159 PA0159 probable transcriptional regulator (NCBI) 49, 268
PA0429 PA0429 hypothetical protein (NCBI) 274, 480
PA0927 ldhA D-lactate dehydrogenase (fermentative) (NCBI) 49, 98
PA1335 PA1335 probable two-component response regulator (NCBI) 49, 215
PA1336 PA1336 probable two-component sensor (NCBI) 49, 215
PA1611 PA1611 probable sensor/response regulator hybrid (NCBI) 198, 480
PA1612 PA1612 hypothetical protein (NCBI) 198, 480
PA1726 bglX periplasmic beta-glucosidase (NCBI) 49, 62
PA1811 PA1811 probable solute-binding protein (NCBI) 49, 380
PA2529 PA2529 hypothetical protein (NCBI) 49, 540
PA2585 uvrC excinuclease ABC subunit C (NCBI) 49, 480
PA2683 PA2683 serine/threonine dehydratase (NCBI) 49, 268
PA2873 PA2873 hypothetical protein (NCBI) 49, 387
PA2908 cbiD cobalt-precorrin-6A synthase (NCBI) 49, 442
PA2909 PA2909 precorrin-6x reductase (NCBI) 49, 355
PA2948 cobM precorrin-3 methylase (NCBI) 49, 493
PA3074 PA3074 hypothetical protein (NCBI) 49, 81
PA3076 PA3076 hypothetical protein (NCBI) 49, 295
PA3247 PA3247 putative aminopeptidase 2 (NCBI) 442, 480
PA3673 plsB glycerol-3-phosphate acyltransferase (NCBI) 312, 480
PA3694 PA3694 hypothetical protein (NCBI) 380, 480
PA3863 PA3863 hypothetical protein (NCBI) 49, 517
PA4109 ampR transcriptional regulator AmpR (NCBI) 49, 268
PA4283 recD exodeoxyribonuclease V alpha chain (NCBI) 49, 483
PA4284 recB exodeoxyribonuclease V beta chain (NCBI) 49, 130
PA4285 recC exodeoxyribonuclease V gamma chain (NCBI) 49, 60
PA4546 pilS two-component sensor PilS (NCBI) 78, 480
PA4547 pilR two-component response regulator PilR (NCBI) 81, 480
PA4579 PA4579 hypothetical protein (NCBI) 49, 191
PA4669 ipk 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (NCBI) 49, 480
PA4688 hitB iron (III)-transport system permease HitB (NCBI) 49, 293
PA4794 PA4794 hypothetical protein (NCBI) 49, 480
PA4795 PA4795 hypothetical protein (NCBI) 49, 480
PA4796 PA4796 hypothetical protein (NCBI) 49, 53
PA4807 selB selenocysteine-specific elongation factor (NCBI) 49, 62
PA4863 PA4863 hypothetical protein (NCBI) 49, 540
PA4959 PA4959 hypothetical protein (NCBI) 82, 480
PA4964 parC DNA topoisomerase IV subunit A (NCBI) 49, 442
PA4966 PA4966 hypothetical protein (NCBI) 49, 130
PA5135 PA5135 hypothetical protein (NCBI) 480, 493
PA5165 PA5165 probable two-component sensor (NCBI) 49, 130
PA5250 PA5250 hypothetical protein (NCBI) 151, 480
PA5280 sss site-specific recombinase Sss (NCBI) 49, 62
PA5321 dut deoxyuridine 5'-triphosphate nucleotidohydrolase (NCBI) 174, 480
PA5345 recG ATP-dependent DNA helicase RecG (NCBI) 198, 480
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 PA4669
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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