Organism : Pseudomonas aeruginosa | Module List :
PA2681

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2681
(Mouseover regulator name to see its description)

PA2681 is regulated by 33 influences and regulates 7 modules.
Regulators for PA2681 (33)
Regulator Module Operator
PA0527 190 tf
PA0701 190 tf
PA1145 190 tf
PA1399 190 tf
PA1599 190 tf
PA1998 190 tf
PA2681 190 tf
PA2696 190 tf
PA2848 190 tf
PA3565 190 tf
PA3830 190 tf
PA3845 190 tf
PA4270 190 tf
PA5116 190 tf
PA5344 190 tf
PA0163 235 tf
PA0306 235 tf
PA0701 235 tf
PA1347 235 tf
PA1399 235 tf
PA2312 235 tf
PA2354 235 tf
PA2376 235 tf
PA2432 235 tf
PA2447 235 tf
PA2497 235 tf
PA2510 235 tf
PA2681 235 tf
PA2838 235 tf
PA3321 235 tf
PA3594 235 tf
PA5293 235 tf
PA5562 235 tf

Warning: PA2681 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
3208 3.00e-07 AcAgGaTcCGCctAgTcTATC
Loader icon
3209 2.10e-02 aCtcTAcTcctTGCg.taCgccAA
Loader icon
3298 4.60e-08 aAGGtaTa.caac.aTtaATtTCc
Loader icon
3299 5.60e-10 a.Ttt..GctAT.c.ttTcgacaA
Loader icon
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 PA2681

PA2681 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA2681

PA2681 has total of 48 gene neighbors in modules 190, 235
Gene neighbors (48)
Gene Common Name Description Module membership
PA0192 PA0192 probable TonB-dependent receptor (NCBI) 235, 289
PA0476 PA0476 probable permease (NCBI) 235, 532
PA0710 gloA2 lactoylglutathione lyase (NCBI) 190, 434
PA0712 PA0712 hypothetical protein (NCBI) 48, 190
PA1134 PA1134 hypothetical protein (NCBI) 119, 190
PA1223 PA1223 probable transcriptional regulator (NCBI) 235, 359
PA1224 PA1224 probable NAD(P)H dehydrogenase (NCBI) 235, 359
PA1405 PA1405 probable helicase (NCBI) 190, 355
PA1844 PA1844 hypothetical protein (NCBI) 235, 375
PA1979 PA1979 probable two-component sensor (NCBI) 235, 434
PA2055 PA2055 probable major facilitator superfamily (MFS) transporter (NCBI) 24, 235
PA2309 PA2309 hypothetical protein (NCBI) 22, 235
PA2325 PA2325 hypothetical protein (NCBI) 235, 287
PA2350 PA2350 probable ATP-binding component of ABC transporter (NCBI) 235, 446
PA2351 PA2351 probable permease of ABC transporter (NCBI) 235, 446
PA2435 PA2435 probable cation-transporting P-type ATPase (NCBI) 235, 334
PA2475 PA2475 probable cytochrome P450 (NCBI) 190, 290
PA2497 PA2497 probable transcriptional regulator (NCBI) 235, 290
PA2499 PA2499 probable deaminase (NCBI) 235, 290
PA2500 PA2500 probable major facilitator superfamily (MFS) transporter (NCBI) 235, 290
PA2531 PA2531 putative aminotransferase (NCBI) 74, 190
PA2679 PA2679 hypothetical protein (NCBI) 189, 190
PA2680 PA2680 probable quinone oxidoreductase (NCBI) 190, 473
PA2681 PA2681 probable transcriptional regulator (NCBI) 190, 235
PA2719 PA2719 hypothetical protein (NCBI) 190, 386
PA2752 PA2752 hypothetical protein (NCBI) 235, 542
PA2782 PA2782 hypothetical protein (NCBI) 190, 383
PA2783 PA2783 hypothetical protein (NCBI) 190, 355
PA2869 PA2869 hypothetical protein (NCBI) 190, 461
PA2870 PA2870 hypothetical protein (NCBI) 190, 461
PA2925 hisM histidine transport system permease HisM (NCBI) 235, 359
PA2928 PA2928 hypothetical protein (NCBI) 30, 190
PA2941 PA2941 hypothetical protein (NCBI) 156, 190
PA2984 PA2984 hypothetical protein (NCBI) 97, 190
PA3064 pelA hypothetical protein (NCBI) 235, 401
PA3320 PA3320 hypothetical protein (NCBI) 235, 359
PA3321 PA3321 probable transcriptional regulator (NCBI) 235, 326
PA3565 PA3565 probable transcriptional regulator (NCBI) 190, 461
PA3844 PA3844 hypothetical protein (NCBI) 88, 190
PA3845 PA3845 probable transcriptional regulator (NCBI) 44, 190
PA3897 PA3897 hypothetical protein (NCBI) 190, 534
PA3985 PA3985 hypothetical protein (NCBI) 30, 190
PA4081 cupB6 fimbrial subunit CupB6 (NCBI) 235, 536
PA4087 PA4087 hypothetical protein (NCBI) 235, 285
PA5150 PA5150 probable short-chain dehydrogenase (NCBI) 190, 351
PA5151 PA5151 hypothetical protein (NCBI) 190, 351
PA5254 PA5254 probable peptidyl-prolyl cis-trans isomerase, FkbP-type (NCBI) 235, 333
PA5439 PA5439 probable glucose-6-phosphate dehydrogenase (NCBI) 190, 469
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 PA2681
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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