Organism : Pseudomonas aeruginosa | Module List :
PA1544 anr

transcriptional regulator Anr (NCBI)

CircVis
Functional Annotations (4)
Function System
cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1544
(Mouseover regulator name to see its description)

PA1544 is regulated by 27 influences and regulates 27 modules.
Regulators for PA1544 anr (27)
Regulator Module Operator
PA0393 524 tf
PA0416 524 tf
PA0763 524 tf
PA0797 524 tf
PA0815 524 tf
PA1544 524 tf
PA2016 524 tf
PA2737 524 tf
PA3689 524 tf
PA4169 524 tf
PA5253 524 tf
PA5301 524 tf
PA5374 524 tf
PA0456 327 tf
PA0610 327 tf
PA0652 327 tf
PA1099 327 tf
PA1159 327 tf
PA1544 327 tf
PA2849 327 tf
PA2885 327 tf
PA3965 327 tf
PA4315 327 tf
PA4745 327 tf
PA4755 327 tf
PA5253 327 tf
PA5374 327 tf

Warning: PA1544 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
3480 1.40e-03 tA.aattggt.aTtATTt
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3481 3.30e-01 TttttgtCGgGctTTttttcCC
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3862 7.00e-11 tGTtcattatttttAACa.aaac
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3863 3.50e-01 aT.Ttgtt.TTcTgG
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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 PA1544

PA1544 is enriched for 4 functions in 3 categories.
Module neighborhood information for PA1544

PA1544 has total of 36 gene neighbors in modules 327, 524
Gene neighbors (36)
Gene Common Name Description Module membership
PA0265 gabD succinate-semialdehyde dehydrogenase (NCBI) 238, 524
PA0266 gabT 4-aminobutyrate aminotransferase (NCBI) 238, 524
PA0296 PA0296 probable glutamine synthetase (NCBI) 238, 524
PA0297 spuA probable glutamine amidotransferase (NCBI) 238, 524
PA0298 spuB probable glutamine synthetase (NCBI) 238, 524
PA0299 spuC putrescine aminotransferase (NCBI) 238, 524
PA0432 sahH S-adenosyl-L-homocysteine hydrolase (NCBI) 19, 327
PA0456 PA0456 probable cold-shock protein (NCBI) 210, 327
PA1544 anr transcriptional regulator Anr (NCBI) 327, 524
PA1742 PA1742 amidotransferase (NCBI) 238, 524
PA2016 gnyR Regulatory gene of gnyRDBHAL cluster, GnyR (NCBI) 145, 524
PA2604 PA2604 hypothetical protein (NCBI) 376, 524
PA2776 PA2776 hypothetical protein (NCBI) 238, 524
PA2830 htpX heat shock protein HtpX (NCBI) 393, 524
PA3356 PA3356 hypothetical protein (NCBI) 238, 524
PA3357 dsdA D-serine dehydratase (NCBI) 420, 524
PA3531 bfrB bacterioferritin (NCBI) 296, 327
PA3533 PA3533 hypothetical protein (NCBI) 6, 327
PA3940 PA3940 probable DNA binding protein (NCBI) 6, 327
PA4395 PA4395 hypothetical protein (NCBI) 6, 327
PA4944 hfq RNA-binding protein Hfq (NCBI) 182, 327
PA4971 aspP adenosine diphosphate sugar pyrophosphatase (NCBI) 327, 368
PA5068 tatA twin argininte translocase protein A (NCBI) 182, 327
PA5300 cycB cytochrome c5 (NCBI) 281, 327
PA5301 PA5301 probable transcriptional regulator (NCBI) 238, 524
PA5303 PA5303 hypothetical protein (NCBI) 238, 327
PA5304 dadA D-amino acid dehydrogenase small subunit (NCBI) 238, 327
PA5312 PA5312 probable aldehyde dehydrogenase (NCBI) 238, 524
PA5313 PA5313 probable pyridoxal-dependent aminotransferase (NCBI) 238, 524
PA5372 betA choline dehydrogenase (NCBI) 524, 546
PA5373 betB betaine aldehyde dehydrogenase (NCBI) 327, 524
PA5374 betI transcriptional regulator BetI (NCBI) 327, 524
PA5489 dsbA thiol:disulfide interchange protein DsbA (NCBI) 6, 327
PA5490 cc4 cytochrome c4 precursor (NCBI) 165, 327
PA5505 PA5505 probable TonB-dependent receptor (NCBI) 327, 543
PA5528 PA5528 hypothetical protein (NCBI) 8, 327
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 PA1544
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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