Organism : Pseudomonas aeruginosa | Module List :
PA2961 holB

DNA polymerase III subunit delta (NCBI)

CircVis
Functional Annotations (14)
Function System
ATPase involved in DNA replication cog/ cog
DNA binding go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
ATP binding go/ molecular_function
nucleus go/ cellular_component
DNA replication go/ biological_process
3'-5' exonuclease activity go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
DNA replication kegg/ kegg pathway
Mismatch repair kegg/ kegg pathway
Homologous recombination kegg/ kegg pathway
holB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2961
(Mouseover regulator name to see its description)

PA2961 is regulated by 41 influences and regulates 0 modules.
Regulators for PA2961 holB (41)
Regulator Module Operator
PA0815 1 tf
PA0961 1 tf
PA1422 1 tf
PA1853 1 tf
PA2556 1 tf
PA2586 1 tf
PA2704 1 tf
PA2859 1 tf
PA2957 1 tf
PA3002 1 tf
PA3174 1 tf
PA3285 1 tf
PA3604 1 tf
PA3778 1 tf
PA3804 1 tf
PA4052 1 tf
PA4074 1 tf
PA4184 1 tf
PA4530 1 tf
PA4745 1 tf
PA5253 1 tf
PA5356 1 tf
PA5403 1 tf
PA5550 1 tf
PA5562 1 tf
PA0179 396 tf
PA0275 396 tf
PA0890 396 tf
PA0893 396 tf
PA2622 396 tf
PA2718 396 tf
PA3002 396 tf
PA3563 396 tf
PA3604 396 tf
PA3804 396 tf
PA4269 396 tf
PA4275 396 tf
PA4890 396 tf
PA5166 396 tf
PA5550 396 tf
PA5562 396 tf

Warning: PA2961 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
2838 4.10e-03 aAG.gcgccATT.TAg
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2839 5.40e+00 AATTAGCcataaACCgcTgTaA
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3616 5.30e+03 tAACgAaAAGA
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3617 1.30e+04 ATaATaaGGa
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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 PA2961

PA2961 is enriched for 14 functions in 3 categories.
Enrichment Table (14)
Function System
ATPase involved in DNA replication cog/ cog
DNA binding go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
ATP binding go/ molecular_function
nucleus go/ cellular_component
DNA replication go/ biological_process
3'-5' exonuclease activity go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
DNA replication kegg/ kegg pathway
Mismatch repair kegg/ kegg pathway
Homologous recombination kegg/ kegg pathway
holB tigr/ tigrfam
Module neighborhood information for PA2961

PA2961 has total of 36 gene neighbors in modules 1, 396
Gene neighbors (36)
Gene Common Name Description Module membership
PA0437 codA cytosine deaminase (NCBI) 260, 396
PA0549 PA0549 hypothetical protein (NCBI) 353, 396
PA0889 aotQ arginine/ornithine transport protein AotQ (NCBI) 353, 396
PA1032 PA1032 probable penicillin amidase (NCBI) 78, 396
PA1529 lig DNA ligase (NCBI) 14, 396
PA1678 PA1678 probable DNA methylase (NCBI) 1, 306
PA1758 pabB para-aminobenzoate synthase component I (NCBI) 1, 517
PA1926 PA1926 hypothetical protein (NCBI) 396, 511
PA2449 PA2449 probable transcriptional regulator (NCBI) 1, 135
PA2453 PA2453 hypothetical protein (NCBI) 1, 281
PA2959 PA2959 hypothetical protein (NCBI) 1, 195
PA2960 pilZ type 4 fimbrial biogenesis protein PilZ (NCBI) 1, 195
PA2961 holB DNA polymerase III subunit delta (NCBI) 1, 396
PA2962 tmk thymidylate kinase (NCBI) 1, 62
PA2963 PA2963 hypothetical protein (NCBI) 1, 274
PA2964 pabC 4-amino-4-deoxychorismate lyase (NCBI) 1, 396
PA2966 acpP acyl carrier protein (NCBI) 1, 210
PA2969 plsX fatty acid/phospholipid synthesis protein (NCBI) 1, 207
PA2972 PA2972 Maf-like protein (NCBI) 1, 299
PA2977 murB UDP-N-acetylenolpyruvoylglucosamine reductase (NCBI) 1, 517
PA2978 ptpA phosphotyrosine protein phosphatase (NCBI) 1, 14
PA2981 lpxK tetraacyldisaccharide 4'-kinase (NCBI) 1, 14
PA3490 PA3490 electron transport complex protein RnfB (NCBI) 306, 396
PA3492 PA3492 hypothetical protein (NCBI) 43, 396
PA3493 PA3493 hypothetical protein (NCBI) 396, 421
PA3494 PA3494 NADH-ubiquinone oxidoreductase (NCBI) 396, 421
PA3633 ispD 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (NCBI) 312, 396
PA3634 PA3634 hypothetical protein (NCBI) 14, 396
PA3658 glnD PII uridylyl-transferase (NCBI) 396, 421
PA3659 PA3659 hypothetical protein (NCBI) 396, 421
PA4011 PA4011 hypothetical protein (NCBI) 130, 396
PA4046 PA4046 hypothetical protein (NCBI) 1, 126
PA4619 PA4619 probable c-type cytochrome (NCBI) 1, 517
PA4620 PA4620 hypothetical protein (NCBI) 1, 517
PA4728 folK 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase (NCBI) 130, 396
PA5050 priA primosome assembly protein PriA (NCBI) 374, 396
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 PA2961
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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