Organism : Pseudomonas aeruginosa | Module List :
PA3002 mfd

transcription-repair coupling protein Mfd (NCBI)

CircVis
Functional Annotations (9)
Function System
Transcription-repair coupling factor (superfamily II helicase) cog/ cog
damaged DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
DNA repair go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
ATP-dependent helicase activity go/ molecular_function
Nucleotide excision repair kegg/ kegg pathway
mfd tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3002
(Mouseover regulator name to see its description)

PA3002 is regulated by 26 influences and regulates 105 modules.
Regulators for PA3002 mfd (26)
Regulator Module Operator
PA0393 18 tf
PA0576 18 tf
PA0893 18 tf
PA1526 18 tf
PA3002 18 tf
PA3711 18 tf
PA3804 18 tf
PA4057 18 tf
PA4269 18 tf
PA4530 18 tf
PA5344 18 tf
PA5562 18 tf
PA0763 43 tf
PA0893 43 tf
PA0961 43 tf
PA1335 43 tf
PA2383 43 tf
PA2766 43 tf
PA2859 43 tf
PA3002 43 tf
PA3804 43 tf
PA4269 43 tf
PA4270 43 tf
PA4275 43 tf
PA5356 43 tf
PA5562 43 tf

Warning: PA3002 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
2872 2.70e-03 acATaATAaCaacTcttC.cTcgA
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2873 7.70e-02 AcctaCctTTCAtGtGt
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2918 6.60e-01 aaagaa.GcccggcATTaTaaa
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2919 8.60e+02 AtgaTtgG.GAtttt
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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 PA3002

PA3002 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Transcription-repair coupling factor (superfamily II helicase) cog/ cog
damaged DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
DNA repair go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
ATP-dependent helicase activity go/ molecular_function
Nucleotide excision repair kegg/ kegg pathway
mfd tigr/ tigrfam
Module neighborhood information for PA3002

PA3002 has total of 36 gene neighbors in modules 18, 43
Gene neighbors (36)
Gene Common Name Description Module membership
PA0374 ftsE cell division protein FtsE (NCBI) 18, 552
PA0375 ftsX cell division protein FtsX (NCBI) 18, 478
PA0392 PA0392 hypothetical protein (NCBI) 18, 499
PA0590 apaH diadenosinetetraphosphatase (NCBI) 18, 464
PA1478 PA1478 hypothetical protein (NCBI) 43, 421
PA1482 ccmH cytochrome C-type biogenesis protein CcmH (NCBI) 43, 350
PA1483 cycH cytochrome c-type biogenesis protein (NCBI) 43, 421
PA2973 PA2973 probable peptidase (NCBI) 18, 261
PA2992 PA2992 hypothetical protein (NCBI) 43, 552
PA2994 nqrF Na(+)-translocating NADH-quinone reductase subunit F (NCBI) 43, 427
PA2998 nqrB Na(+)-translocating NADH-quinone reductase subunit B (NCBI) 43, 395
PA3002 mfd transcription-repair coupling protein Mfd (NCBI) 18, 43
PA3166 pheA chorismate mutase (NCBI) 18, 403
PA3199 PA3199 hypothetical protein (NCBI) 18, 390
PA3200 PA3200 hypothetical protein (NCBI) 18, 31
PA3201 PA3201 putative intracellular septation protein (NCBI) 18, 398
PA3202 PA3202 hypothetical protein (NCBI) 18, 513
PA3482 metG methionyl-tRNA synthetase (NCBI) 18, 198
PA3491 PA3491 electron transport complex protein RnfC (NCBI) 43, 421
PA3492 PA3492 hypothetical protein (NCBI) 43, 396
PA3495 nth endonuclease III (NCBI) 43, 421
PA3625 surE stationary phase survival protein SurE (NCBI) 18, 228
PA3735 thrC threonine synthase (NCBI) 43, 350
PA3769 guaA bifunctional GMP synthase/glutamine amidotransferase protein (NCBI) 43, 204
PA3989 holA DNA polymerase III subunit delta (NCBI) 18, 81
PA4557 lytB 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (NCBI) 43, 350
PA4559 lspA signal peptidase II (NCBI) 43, 350
PA4560 ileS isoleucyl-tRNA synthetase (NCBI) 43, 106
PA5065 ubiB ubiquinone biosynthetic protein UbiB (NCBI) 43, 387
PA5074 PA5074 probable ATP-binding component of ABC transporter (NCBI) 43, 151
PA5223 ubiH 2-octaprenyl-6-methoxyphenyl hydroxylase (NCBI) 18, 81
PA5498 PA5498 probable adhesin (NCBI) 18, 276
PA5499 np20 transcriptional regulator np20 (NCBI) 18, 276
PA5500 znuC zinc transport protein ZnuC (NCBI) 18, 276
PA5501 znuB permease of ABC zinc transporter ZnuB (NCBI) 18, 276
PA5502 PA5502 hypothetical protein (NCBI) 18, 276
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 PA3002
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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