Organism : Pseudomonas aeruginosa | Module List :
PA4984

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4984
(Mouseover regulator name to see its description)

PA4984 is regulated by 37 influences and regulates 11 modules.
Regulators for PA4984 (37)
Regulator Module Operator
PA0780 245 tf
PA0873 245 tf
PA1309 245 tf
PA1335 245 tf
PA1359 245 tf
PA1607 245 tf
PA2020 245 tf
PA2032 245 tf
PA2885 245 tf
PA2957 245 tf
PA3220 245 tf
PA3508 245 tf
PA3594 245 tf
PA3604 245 tf
PA3711 245 tf
PA3782 245 tf
PA3830 245 tf
PA4203 245 tf
PA4764 245 tf
PA4906 245 tf
PA4984 245 tf
PA4989 245 tf
PA5253 245 tf
PA0032 507 tf
PA0279 507 tf
PA1226 507 tf
PA1374 507 tf
PA1399 507 tf
PA1467 507 tf
PA1998 507 tf
PA2050 507 tf
PA3133 507 tf
PA4270 507 tf
PA4341 507 tf
PA4581 507 tf
PA4989 507 tf
PA5431 507 tf
Regulated by PA4984 (11)
Module Residual Genes
15 0.42 12
29 0.34 10
70 0.56 30
245 0.56 39
273 0.49 17
274 0.51 18
300 0.44 18
436 0.53 18
468 0.55 24
531 0.31 11
539 0.28 12
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3318 3.30e+03 gCttTTCC
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3319 3.30e+04 GAAATcCAt
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3828 4.50e+02 cgG.TTTTTcC
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3829 3.30e+04 CTAcaAaaA.tAAcata..AA
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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 PA4984

PA4984 is enriched for 5 functions in 3 categories.
Module neighborhood information for PA4984

PA4984 has total of 65 gene neighbors in modules 245, 507
Gene neighbors (65)
Gene Common Name Description Module membership
PA0211 mdcD acetyl-CoA carboxylase beta subunit (NCBI) 24, 507
PA0215 PA0215 probable transporter (NCBI) 330, 507
PA0216 PA0216 probable transporter (NCBI) 24, 507
PA0255 PA0255 hypothetical protein (NCBI) 170, 245
PA0279 PA0279 probable transcriptional regulator (NCBI) 30, 507
PA0307 PA0307 hypothetical protein (NCBI) 72, 245
PA0360 PA0360 hypothetical protein (NCBI) 170, 245
PA0464 creC two-component sensor CreC (NCBI) 351, 507
PA0488 PA0488 hypothetical protein (NCBI) 330, 507
PA0581 PA0581 hypothetical protein (NCBI) 507, 541
PA0584 cca tRNA nucleotidyl transferase (NCBI) 245, 306
PA0600 PA0600 probable two-component sensor (NCBI) 175, 245
PA0780 pruR proline utilization regulator (NCBI) 245, 550
PA0787 PA0787 hypothetical protein (NCBI) 245, 537
PA1226 PA1226 probable transcriptional regulator (NCBI) 507, 542
PA1242 PA1242 hypothetical protein (NCBI) 245, 280
PA1325 PA1325 hypothetical protein (NCBI) 33, 245
PA1401 PA1401 hypothetical protein (NCBI) 295, 507
PA1411 PA1411 hypothetical protein (NCBI) 246, 507
PA1451 PA1451 hypothetical protein (NCBI) 97, 245
PA1466 PA1466 hypothetical protein (NCBI) 266, 507
PA1468 PA1468 hypothetical protein (NCBI) 44, 507
PA1469 PA1469 hypothetical protein (NCBI) 245, 337
PA1576 PA1576 probable 3-hydroxyisobutyrate dehydrogenase (NCBI) 63, 245
PA1672 PA1672 hypothetical protein (NCBI) 245, 397
PA1841 PA1841 hypothetical protein (NCBI) 181, 245
PA1960 PA1960 hypothetical protein (NCBI) 245, 438
PA2027 PA2027 hypothetical protein (NCBI) 79, 507
PA2028 PA2028 probable transcriptional regulator (NCBI) 268, 507
PA2032 PA2032 probable transcriptional regulator (NCBI) 192, 245
PA2125 PA2125 probable aldehyde dehydrogenase (NCBI) 23, 507
PA2558 PA2558 probable transport protein (NCBI) 48, 245
PA2563 PA2563 probable sulfate transporter (NCBI) 438, 507
PA2695 PA2695 hypothetical protein (NCBI) 229, 245
PA2712 PA2712 hypothetical protein (NCBI) 245, 337
PA2842 PA2842 hypothetical protein (NCBI) 245, 374
PA2860 PA2860 hypothetical protein (NCBI) 229, 245
PA3015 PA3015 hypothetical protein (NCBI) 245, 313
PA3178 PA3178 hypothetical protein (NCBI) 229, 245
PA3265 PA3265 probable transporter (NCBI) 20, 507
PA3782 PA3782 probable transcriptional regulator (NCBI) 226, 245
PA3825 PA3825 hypothetical protein (NCBI) 245, 266
PA3829 PA3829 hypothetical protein (NCBI) 30, 507
PA4114 PA4114 spermidine acetyltransferase (NCBI) 9, 245
PA4334 PA4334 probable transport protein (NCBI) 30, 507
PA4374 PA4374 probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein precursor (NCBI) 245, 313
PA4383 PA4383 hypothetical protein (NCBI) 245, 283
PA4531 PA4531 hypothetical protein (NCBI) 245, 321
PA4656 PA4656 hypothetical protein (NCBI) 243, 245
PA4716 PA4716 hypothetical protein (NCBI) 196, 245
PA4780 PA4780 hypothetical protein (NCBI) 245, 248
PA4862 PA4862 probable ATP-binding component of ABC transporter (NCBI) 386, 507
PA4982 PA4982 probable two-component sensor (NCBI) 497, 507
PA4983 PA4983 probable two-component response regulator (NCBI) 245, 469
PA4984 PA4984 probable transcriptional regulator (NCBI) 245, 507
PA5081 PA5081 hypothetical protein (NCBI) 283, 507
PA5145 PA5145 hypothetical protein (NCBI) 245, 313
PA5200 ompR two-component response regulator OmpR (NCBI) 245, 253
PA5248 PA5248 hypothetical protein (NCBI) 245, 383
PA5249 PA5249 hypothetical protein (NCBI) 507, 550
PA5275 cyaY frataxin-like protein (NCBI) 243, 245
PA5287 amtB ammonium transporter AmtB (NCBI) 236, 245
PA5327 PA5327 probable oxidoreductase (NCBI) 180, 507
PA5431 PA5431 probable transcriptional regulator (NCBI) 497, 507
PA5537 PA5537 hypothetical protein (NCBI) 134, 507
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 PA4984
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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