Organism : Pseudomonas aeruginosa | Module List :
PA4988 waaA

3-deoxy-D-manno-octulosonic-acid transferase (NCBI)

CircVis
Functional Annotations (7)
Function System
3-deoxy-D-manno-octulosonic-acid transferase cog/ cog
sugar binding go/ molecular_function
carbohydrate metabolic process go/ biological_process
biosynthetic process go/ biological_process
transferase activity go/ molecular_function
Lipopolysaccharide biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4988
(Mouseover regulator name to see its description)

PA4988 is regulated by 43 influences and regulates 0 modules.
Regulators for PA4988 waaA (43)
Regulator Module Operator
PA0116 422 tf
PA0155 422 tf
PA0236 422 tf
PA0475 422 tf
PA0707 422 tf
PA1141 422 tf
PA1197 422 tf
PA1241 422 tf
PA1290 422 tf
PA1312 422 tf
PA1397 422 tf
PA1490 422 tf
PA1853 422 tf
PA2047 422 tf
PA2115 422 tf
PA2802 422 tf
PA3067 422 tf
PA3322 422 tf
PA3622 422 tf
PA3921 422 tf
PA4077 422 tf
PA4547 422 tf
PA4853 422 tf
PA5356 422 tf
PA5382 422 tf
PA5550 422 tf
PA0032 266 tf
PA0163 266 tf
PA0253 266 tf
PA1359 266 tf
PA2050 266 tf
PA2766 266 tf
PA3002 266 tf
PA3133 266 tf
PA3364 266 tf
PA3423 266 tf
PA4354 266 tf
PA4363 266 tf
PA4989 266 tf
PA5085 266 tf
PA5253 266 tf
PA5342 266 tf
PA5431 266 tf

Warning: PA4988 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
3360 3.60e-19 aa.AaAGat.g.TAaCgAttgt
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3361 3.60e-07 AcCtGCGGatg.aCgagggAcCCg
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3666 4.80e-04 aaaAagGGgc.cgAct.TagC
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3667 2.60e+01 AATGTAaagcttGCTTgaCaAAGA
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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 PA4988

PA4988 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
3-deoxy-D-manno-octulosonic-acid transferase cog/ cog
sugar binding go/ molecular_function
carbohydrate metabolic process go/ biological_process
biosynthetic process go/ biological_process
transferase activity go/ molecular_function
Lipopolysaccharide biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for PA4988

PA4988 has total of 44 gene neighbors in modules 266, 422
Gene neighbors (44)
Gene Common Name Description Module membership
PA0164 PA0164 probable gamma-glutamyltranspeptidase (NCBI) 240, 266
PA0239 PA0239 hypothetical protein (NCBI) 266, 536
PA0310 PA0310 hypothetical protein (NCBI) 48, 422
PA0749 PA0749 hypothetical protein (NCBI) 68, 266
PA0989 PA0989 hypothetical protein (NCBI) 266, 323
PA1116 PA1116 hypothetical protein (NCBI) 230, 422
PA1309 PA1309 probable transcriptional regulator (NCBI) 266, 438
PA1394 PA1394 hypothetical protein (NCBI) 372, 422
PA1395 PA1395 hypothetical protein (NCBI) 372, 422
PA1450 PA1450 hypothetical protein (NCBI) 266, 344
PA1466 PA1466 hypothetical protein (NCBI) 266, 507
PA1734 PA1734 hypothetical protein (NCBI) 178, 266
PA1735 PA1735 hypothetical protein (NCBI) 178, 266
PA1958 PA1958 probable transporter (NCBI) 58, 422
PA2766 PA2766 probable transcriptional regulator (NCBI) 266, 323
PA2767 PA2767 probable enoyl-CoA hydratase/isomerase (NCBI) 266, 323
PA2768 PA2768 hypothetical protein (NCBI) 266, 323
PA2876 pyrF orotidine 5'-phosphate decarboxylase (NCBI) 247, 422
PA2956 PA2956 hypothetical protein (NCBI) 344, 422
PA3050 pyrD dihydroorotate dehydrogenase (NCBI) 111, 422
PA3276 PA3276 hypothetical protein (NCBI) 255, 266
PA3825 PA3825 hypothetical protein (NCBI) 245, 266
PA3826 PA3826 hypothetical protein (NCBI) 266, 375
PA3967 PA3967 hypothetical protein (NCBI) 422, 520
PA4013 PA4013 hypothetical protein (NCBI) 351, 422
PA4075 PA4075 hypothetical protein (NCBI) 229, 422
PA4076 PA4076 hypothetical protein (NCBI) 58, 422
PA4077 PA4077 probable transcriptional regulator (NCBI) 58, 422
PA4113 PA4113 sugar efflux transporter (NCBI) 377, 422
PA4167 PA4167 probable oxidoreductase (NCBI) 175, 266
PA4233 PA4233 probable major facilitator superfamily (MFS) transporter (NCBI) 299, 422
PA4445 PA4445 hypothetical protein (NCBI) 299, 422
PA4644 PA4644 hypothetical protein (NCBI) 65, 422
PA4988 waaA 3-deoxy-D-manno-octulosonic-acid transferase (NCBI) 266, 422
PA4989 PA4989 probable transcriptional regulator (NCBI) 266, 335
PA4990 PA4990 SMR multidrug efflux transporter (NCBI) 23, 266
PA4991 PA4991 hypothetical protein (NCBI) 58, 266
PA4992 PA4992 hypothetical protein (NCBI) 253, 266
PA5034 hemE uroporphyrinogen decarboxylase (NCBI) 335, 422
PA5085 PA5085 probable transcriptional regulator (NCBI) 220, 266
PA5193 hslO Hsp33-like chaperonin (NCBI) 422, 520
PA5311 PA5311 probable major facilitator superfamily (MFS) transporter (NCBI) 266, 335
PA5442 PA5442 hypothetical protein (NCBI) 266, 438
PA5529 PA5529 probable sodium/proton antiporter (NCBI) 220, 422
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 PA4988
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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