Organism : Pseudomonas aeruginosa | Module List :
PA4906

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of fatty acid metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4906
(Mouseover regulator name to see its description)

PA4906 is regulated by 15 influences and regulates 13 modules.
Regulators for PA4906 (15)
Regulator Module Operator
PA0116 253 tf
PA0191 253 tf
PA0393 253 tf
PA0873 253 tf
PA0893 253 tf
PA1050 253 tf
PA2423 253 tf
PA3094 253 tf
PA3126 253 tf
PA3477 253 tf
PA3804 253 tf
PA4547 253 tf
PA4906 253 tf
PA5342 253 tf
PA5562 253 tf
Regulated by PA4906 (13)
Module Residual Genes
22 0.45 20
118 0.44 16
156 0.44 25
212 0.61 30
245 0.56 39
253 0.56 35
298 0.21 15
313 0.51 38
353 0.50 21
383 0.67 8
384 0.56 30
515 0.44 18
546 0.54 31
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
2910 5.90e+00 TaaaatgccCgCCCttTtTtC
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2911 2.80e+03 ATAAAT
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3334 3.70e-02 GgTAtaaTgcggcGc..ttcc
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3335 1.10e+01 aGccTT..CcCCg.CC.gCCGc
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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 PA4906

PA4906 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of fatty acid metabolic process go/ biological_process
Module neighborhood information for PA4906

PA4906 has total of 53 gene neighbors in modules 39, 253
Gene neighbors (53)
Gene Common Name Description Module membership
PA0116 PA0116 hypothetical protein (NCBI) 253, 268
PA0338 PA0338 hypothetical protein (NCBI) 34, 39
PA0352 PA0352 probable transporter (NCBI) 39, 230
PA0501 bioF 8-amino-7-oxononanoate synthase (NCBI) 91, 253
PA0502 PA0502 probable biotin biosynthesis protein bioH (NCBI) 91, 253
PA0504 bioD dithiobiotin synthetase (NCBI) 62, 253
PA0556 PA0556 hypothetical protein (NCBI) 14, 253
PA0658 PA0658 probable short-chain dehydrogenase (NCBI) 189, 253
PA0935 PA0935 hypothetical protein (NCBI) 253, 341
PA0951 PA0951 probable ribonuclease (NCBI) 229, 253
PA1050 PA1050 hypothetical protein (NCBI) 162, 253
PA1522 PA1522 hypothetical protein (NCBI) 39, 382
PA1679 PA1679 hypothetical protein (NCBI) 253, 496
PA1682 PA1682 probable MFS metabolite transporter (NCBI) 214, 253
PA1685 masA enolase-phosphatase E-1 (NCBI) 253, 384
PA1973 pqqF pyrroloquinoline quinone biosynthesis protein F (NCBI) 253, 483
PA2018 PA2018 RND multidrug efflux transporter (NCBI) 39, 108
PA2289 PA2289 hypothetical protein (NCBI) 39, 62
PA2868 PA2868 hypothetical protein (NCBI) 39, 432
PA3019 PA3019 probable ATP-binding component of ABC transporter (NCBI) 39, 114
PA3071 PA3071 hypothetical protein (NCBI) 253, 511
PA3075 PA3075 hypothetical protein (NCBI) 253, 511
PA3087 PA3087 hypothetical protein (NCBI) 3, 253
PA3240 PA3240 hypothetical protein (NCBI) 39, 212
PA3241 PA3241 hypothetical protein (NCBI) 253, 483
PA3242 PA3242 lipid A biosynthesis lauroyl acyltransferase (NCBI) 39, 181
PA3271 PA3271 probable two-component sensor (NCBI) 39, 187
PA3676 PA3676 probable Resistance-Nodulation-Cell Division (RND) efflux transporter (NCBI) 39, 550
PA3683 PA3683 hypothetical protein (NCBI) 253, 493
PA3750 PA3750 hypothetical protein (NCBI) 3, 253
PA3853 PA3853 probable transferase (NCBI) 14, 253
PA3963 PA3963 probable transporter (NCBI) 20, 253
PA4162 PA4162 short chain dehydrogenase (NCBI) 39, 320
PA4347 PA4347 hypothetical protein (NCBI) 241, 253
PA4398 PA4398 probable two-component sensor (NCBI) 196, 253
PA4438 PA4438 hypothetical protein (NCBI) 39, 520
PA4584 PA4584 hypothetical protein (NCBI) 39, 157
PA4625 PA4625 hypothetical protein (NCBI) 9, 39
PA4906 PA4906 probable transcriptional regulator (NCBI) 39, 253
PA4992 PA4992 hypothetical protein (NCBI) 253, 266
PA4993 PA4993 hypothetical protein (NCBI) 39, 383
PA5022 PA5022 hypothetical protein (NCBI) 60, 253
PA5137 PA5137 hypothetical protein (NCBI) 39, 218
PA5179 PA5179 probable transcriptional regulator (NCBI) 253, 313
PA5198 PA5198 LD-carboxypeptidase (NCBI) 3, 253
PA5199 envZ two-component sensor EnvZ (NCBI) 220, 253
PA5200 ompR two-component response regulator OmpR (NCBI) 245, 253
PA5202 PA5202 hypothetical protein (NCBI) 253, 451
PA5281 PA5281 probable hydrolase (NCBI) 42, 253
PA5318 PA5318 hypothetical protein (NCBI) 253, 450
PA5342 PA5342 probable transcriptional regulator (NCBI) 170, 253
PA5343 PA5343 hypothetical protein (NCBI) 170, 253
PA5504 PA5504 probable permease of ABC transporter (NCBI) 39, 56
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 PA4906
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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