Organism : Pseudomonas aeruginosa | Module List :
PA1264

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 PA1264
(Mouseover regulator name to see its description)

PA1264 is regulated by 30 influences and regulates 14 modules.
Regulators for PA1264 (30)
Regulator Module Operator
PA1138 192 tf
PA1261 192 tf
PA1312 192 tf
PA1380 192 tf
PA2032 192 tf
PA3420 192 tf
PA3630 192 tf
PA3711 192 tf
PA3830 192 tf
PA4288 192 tf
PA4363 192 tf
PA5032 192 tf
PA5218 192 tf
PA5293 192 tf
PA5431 192 tf
PA5525 192 tf
PA0152 536 tf
PA0477 536 tf
PA1264 536 tf
PA1374 536 tf
PA2838 536 tf
PA3398 536 tf
PA3420 536 tf
PA3433 536 tf
PA3757 536 tf
PA4080 536 tf
PA4184 536 tf
PA4902 536 tf
PA5293 536 tf
PA5382 536 tf

Warning: PA1264 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
3212 1.40e-03 AtAcgTcTgTattcatattg
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3213 3.90e-01 TAtGaAAAAgGAAT
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3884 1.80e-13 A.agAaActATc.gcttcA.t.AT
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3885 6.30e-05 aAaaa.aAgAACagg
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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 PA1264

PA1264 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 PA1264

PA1264 has total of 53 gene neighbors in modules 192, 536
Gene neighbors (53)
Gene Common Name Description Module membership
PA0142 PA0142 hydroxydechloroatrazine ethylaminohydrolase (NCBI) 175, 192
PA0152 pcaQ transcriptional regulator PcaQ (NCBI) 351, 536
PA0153 pcaH protocatechuate 3,4-dioxygenase, beta subunit (NCBI) 292, 536
PA0154 pcaG protocatechuate 3,4-dioxygenase, alpha subunit (NCBI) 196, 536
PA0239 PA0239 hypothetical protein (NCBI) 266, 536
PA0247 pobA 4-hydroxybenzoate 3-monooxygenase (NCBI) 471, 536
PA0347 glpQ glycerophosphoryl diester phosphodiesterase, periplasmic (NCBI) 105, 192
PA0477 PA0477 probable transcriptional regulator (NCBI) 536, 542
PA0529 PA0529 hypothetical protein (NCBI) 34, 536
PA0530 PA0530 probable class III pyridoxal phosphate-dependent aminotransferase (NCBI) 536, 550
PA0531 PA0531 probable glutamine amidotransferase (NCBI) 23, 536
PA0676 PA0676 probable transmembrane sensor (NCBI) 192, 500
PA1138 PA1138 probable transcriptional regulator (NCBI) 192, 373
PA1264 PA1264 probable transcriptional regulator (NCBI) 192, 536
PA1265 PA1265 hypothetical protein (NCBI) 333, 536
PA1282 PA1282 probable major facilitator superfamily (MFS) transporter (NCBI) 92, 192
PA1312 PA1312 probable transcriptional regulator (NCBI) 192, 537
PA1345 PA1345 hypothetical protein (NCBI) 192, 206
PA1503 PA1503 hypothetical protein (NCBI) 192, 425
PA1628 PA1628 probable 3-hydroxyacyl-CoA dehydrogenase (NCBI) 61, 192
PA1635 kdpC potassium-transporting ATPase subunit C (NCBI) 192, 267
PA2032 PA2032 probable transcriptional regulator (NCBI) 192, 245
PA2574 alkB1 alkane-1-monooxygenase (NCBI) 30, 192
PA3387 rhlG beta-ketoacyl reductase (NCBI) 192, 550
PA3398 PA3398 probable transcriptional regulator (NCBI) 536, 542
PA3433 PA3433 probable transcriptional regulator (NCBI) 61, 536
PA3464 PA3464 hypothetical protein (NCBI) 175, 192
PA3561 fruK 1-phosphofructokinase (NCBI) 236, 536
PA3562 PA3562 probable phosphotransferase system enzyme I (NCBI) 236, 536
PA3711 PA3711 probable transcriptional regulator (NCBI) 192, 313
PA3718 PA3718 probable major facilitator superfamily (MFS) transporter (NCBI) 192, 309
PA3733 PA3733 hypothetical protein (NCBI) 175, 192
PA4038 PA4038 hypothetical protein (NCBI) 192, 267
PA4081 cupB6 fimbrial subunit CupB6 (NCBI) 235, 536
PA4082 cupB5 adhesive protein CupB5 (NCBI) 175, 192
PA4092 hpaC 4-hydroxyphenylacetate 3-monooxygenase small chain (NCBI) 192, 337
PA4146 PA4146 hypothetical protein (NCBI) 175, 536
PA4184 PA4184 probable transcriptional regulator (NCBI) 61, 536
PA4287 PA4287 hypothetical protein (NCBI) 177, 192
PA4288 PA4288 probable transcriptional regulator (NCBI) 192, 373
PA4330 PA4330 probable enoyl-CoA hydratase/isomerase (NCBI) 192, 443
PA4351 PA4351 probable acyltransferase (NCBI) 23, 192
PA4363 iciA chromosome replication initiation inhibitor protein (NCBI) 192, 372
PA4586 PA4586 hypothetical protein (NCBI) 192, 497
PA4898 PA4898 probable porin (NCBI) 536, 538
PA4902 PA4902 probable transcriptional regulator (NCBI) 536, 538
PA4980 PA4980 probable enoyl-CoA hydratase/isomerase (NCBI) 125, 536
PA5218 PA5218 probable transcriptional regulator (NCBI) 20, 192
PA5293 PA5293 probable transcriptional regulator (NCBI) 394, 536
PA5381 PA5381 hypothetical protein (NCBI) 192, 345
PA5382 PA5382 probable transcriptional regulator (NCBI) 30, 536
PA5383 PA5383 hypothetical protein (NCBI) 30, 536
PA5388 PA5388 hypothetical protein (NCBI) 236, 536
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 PA1264
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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