Organism : Pseudomonas aeruginosa | Module List :
PA0120

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 PA0120
(Mouseover regulator name to see its description)

PA0120 is regulated by 45 influences and regulates 19 modules.
Regulators for PA0120 (45)
Regulator Module Operator
PA0120 125 tf
PA0191 125 tf
PA0268 125 tf
PA0491 125 tf
PA1003 125 tf
PA1223 125 tf
PA1235 125 tf
PA1430 125 tf
PA1520 125 tf
PA2802 125 tf
PA3381 125 tf
PA3594 125 tf
PA3711 125 tf
PA4363 125 tf
PA4600 125 tf
PA4989 125 tf
PA5293 125 tf
PA5344 125 tf
PA0120 441 tf
PA0121 441 tf
PA0155 441 tf
PA0306 441 tf
PA0763 441 tf
PA0905 441 tf
PA1138 441 tf
PA1754 441 tf
PA2047 441 tf
PA2121 441 tf
PA2692 441 tf
PA2758 441 tf
PA3563 441 tf
PA3622 441 tf
PA3689 441 tf
PA3714 441 tf
PA3921 441 tf
PA4052 441 tf
PA4070 441 tf
PA4157 441 tf
PA4279 441 tf
PA4462 441 tf
PA4890 441 tf
PA5261 441 tf
PA5337 441 tf
PA5403 441 tf
PA5483 441 tf

Warning: PA0120 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
3080 1.00e-10 ataagatcAttctAgaCAATa
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3081 1.10e-07 ACAAcaAgAaAgatg
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3702 9.50e-02 CgcgcTTcGCcgaGG
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3703 1.20e-01 AataCc.gaGtaaAAA
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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 PA0120

PA0120 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 PA0120

PA0120 has total of 42 gene neighbors in modules 125, 441
Gene neighbors (42)
Gene Common Name Description Module membership
PA0119 PA0119 probable dicarboxylate transporter (NCBI) 61, 125
PA0120 PA0120 probable transcriptional regulator (NCBI) 125, 441
PA0121 PA0121 hypothetical protein (NCBI) 61, 441
PA0315 PA0315 hypothetical protein (NCBI) 141, 441
PA0364 PA0364 probable oxidoreductase (NCBI) 361, 441
PA0365 PA0365 hypothetical protein (NCBI) 361, 441
PA0366 PA0366 probable aldehyde dehydrogenase (NCBI) 361, 441
PA0491 PA0491 probable transcriptional regulator (NCBI) 125, 526
PA0492 PA0492 hypothetical protein (NCBI) 125, 526
PA0493 PA0493 acetyl-CoA carboxylase (NCBI) 125, 526
PA0494 PA0494 acetyl-CoA carboxylase (NCBI) 125, 526
PA0495 PA0495 hypothetical protein (NCBI) 125, 526
PA0496 PA0496 hypothetical protein (NCBI) 125, 526
PA0567 PA0567 hypothetical protein (NCBI) 107, 441
PA1106 PA1106 hypothetical protein (NCBI) 361, 441
PA1944 PA1944 hypothetical protein (NCBI) 107, 441
PA2381 PA2381 hypothetical protein (NCBI) 233, 441
PA2486 PA2486 hypothetical protein (NCBI) 441, 494
PA2562 PA2562 hypothetical protein (NCBI) 128, 441
PA2845 PA2845 hypothetical protein (NCBI) 125, 333
PA3687 ppc phosphoenolpyruvate carboxylase (NCBI) 361, 441
PA3712 PA3712 hypothetical protein (NCBI) 208, 441
PA3952 PA3952 hypothetical protein (NCBI) 441, 547
PA4073 PA4073 probable aldehyde dehydrogenase (NCBI) 125, 268
PA4100 PA4100 probable dehydrogenase (NCBI) 125, 285
PA4185 PA4185 probable transcriptional regulator (NCBI) 125, 212
PA4186 PA4186 hypothetical protein (NCBI) 125, 196
PA4187 PA4187 probable major facilitator superfamily (MFS) transporter (NCBI) 125, 267
PA4188 PA4188 hypothetical protein (NCBI) 125, 267
PA4189 PA4189 probable aldehyde dehydrogenase (NCBI) 125, 267
PA4475 PA4475 hypothetical protein (NCBI) 28, 441
PA4477 cafA cytoplasmic axial filament protein (NCBI) 28, 441
PA4597 oprJ Multidrug efflux outer membrane protein OprJ precursor (NCBI) 125, 173
PA4598 mexD Resistance-Nodulation-Cell Division (RND) multidrug efflux transporter MexD (NCBI) 125, 173
PA4599 mexC Resistance-Nodulation-Cell Division (RND) multidrug efflux membrane fusion protein MexC precursor (NCBI) 125, 173
PA4600 nfxB transcriptional regulator NfxB (NCBI) 125, 173
PA4874 PA4874 hypothetical protein (NCBI) 233, 441
PA4977 PA4977 probable acetolactate synthase large subunit (NCBI) 97, 125
PA4978 PA4978 hypothetical protein (NCBI) 97, 125
PA4979 PA4979 probable acyl-CoA dehydrogenase (NCBI) 97, 125
PA4980 PA4980 probable enoyl-CoA hydratase/isomerase (NCBI) 125, 536
PA5530 PA5530 probable MFS dicarboxylate transporter (NCBI) 23, 125
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 PA0120
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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