Organism : Pseudomonas aeruginosa | Module List :
PA1490

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators of sugar metabolism 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 PA1490
(Mouseover regulator name to see its description)

PA1490 is regulated by 34 influences and regulates 7 modules.
Regulators for PA1490 (34)
Regulator Module Operator
PA0123 517 tf
PA0393 517 tf
PA0455 517 tf
PA0961 517 tf
PA1422 517 tf
PA1484 517 tf
PA1490 517 tf
PA2047 517 tf
PA3002 517 tf
PA3604 517 tf
PA3622 517 tf
PA3804 517 tf
PA4853 517 tf
PA4890 517 tf
PA5344 517 tf
PA5562 517 tf
PA0167 384 tf
PA0487 384 tf
PA0780 384 tf
PA0890 384 tf
PA0961 384 tf
PA1099 384 tf
PA1290 384 tf
PA1490 384 tf
PA1859 384 tf
PA3215 384 tf
PA3594 384 tf
PA3604 384 tf
PA3899 384 tf
PA3948 384 tf
PA4021 384 tf
PA4196 384 tf
PA4462 384 tf
PA4906 384 tf

Warning: PA1490 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
3592 7.90e-01 ATCGaTGaAcGaAaaccgGGaatT
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3593 6.90e+02 CCACttCGCCGacGcaAcccC
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3848 4.70e+02 atTTTtcGcCa
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3849 2.30e+04 ATaTCTAAA
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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 PA1490

PA1490 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators of sugar metabolism cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA1490

PA1490 has total of 53 gene neighbors in modules 384, 517
Gene neighbors (53)
Gene Common Name Description Module membership
PA0006 PA0006 hypothetical protein (NCBI) 384, 528
PA0022 PA0022 hypothetical protein (NCBI) 114, 384
PA0267 PA0267 hypothetical protein (NCBI) 170, 517
PA0285 PA0285 hypothetical protein (NCBI) 517, 528
PA0455 dbpA RNA helicase DbpA (NCBI) 306, 517
PA0706 cat chloramphenicol acetyltransferase (NCBI) 384, 501
PA0735 PA0735 hypothetical protein (NCBI) 20, 384
PA0750 ung uracil-DNA glycosylase (NCBI) 123, 384
PA0827 PA0827 hypothetical protein (NCBI) 20, 384
PA0834 PA0834 hypothetical protein (NCBI) 261, 517
PA0902 PA0902 hypothetical protein (NCBI) 170, 384
PA0919 PA0919 hypothetical protein (NCBI) 202, 384
PA0920 PA0920 hypothetical protein (NCBI) 202, 384
PA0921 PA0921 hypothetical protein (NCBI) 202, 384
PA0925 PA0925 hypothetical protein (NCBI) 493, 517
PA1031 PA1031 hypothetical protein (NCBI) 94, 384
PA1042 PA1042 hypothetical protein (NCBI) 3, 384
PA1043 PA1043 hypothetical protein (NCBI) 338, 384
PA1304 PA1304 probable oligopeptidase (NCBI) 499, 517
PA1422 gbuR GbuR (NCBI) 151, 517
PA1490 PA1490 probable transcriptional regulator (NCBI) 384, 517
PA1640 PA1640 hypothetical protein (NCBI) 51, 384
PA1685 masA enolase-phosphatase E-1 (NCBI) 253, 384
PA1748 PA1748 enoyl-CoA hydratase (NCBI) 20, 384
PA1758 pabB para-aminobenzoate synthase component I (NCBI) 1, 517
PA1798 PA1798 probable two-component sensor (NCBI) 384, 499
PA1799 PA1799 probable two-component response regulator (NCBI) 384, 499
PA1840 PA1840 hypothetical protein (NCBI) 181, 384
PA2545 xthA exodeoxyribonuclease III (NCBI) 384, 499
PA2947 PA2947 hypothetical protein (NCBI) 384, 493
PA2977 murB UDP-N-acetylenolpyruvoylglucosamine reductase (NCBI) 1, 517
PA3297 PA3297 probable ATP-dependent helicase (NCBI) 442, 517
PA3338 PA3338 hypothetical protein (NCBI) 384, 499
PA3539 PA3539 hypothetical protein (NCBI) 517, 528
PA3862 PA3862 hypothetical protein (NCBI) 151, 517
PA3863 PA3863 hypothetical protein (NCBI) 49, 517
PA3984 lnt apolipoprotein N-acyltransferase (NCBI) 517, 528
PA3992 PA3992 hypothetical protein (NCBI) 384, 493
PA4376 pncB2 nicotinate phosphoribosyltransferase (NCBI) 337, 384
PA4400 PA4400 hypothetical protein (NCBI) 3, 384
PA4401 PA4401 probable glutathione S-transferase (NCBI) 3, 384
PA4455 PA4455 probable permease of ABC transporter (NCBI) 474, 517
PA4498 PA4498 probable metallopeptidase (NCBI) 131, 517
PA4618 PA4618 hypothetical protein (NCBI) 3, 517
PA4619 PA4619 probable c-type cytochrome (NCBI) 1, 517
PA4620 PA4620 hypothetical protein (NCBI) 1, 517
PA4621 PA4621 probable oxidoreductase (NCBI) 401, 517
PA4642 PA4642 hypothetical protein (NCBI) 354, 384
PA4722 PA4722 hypothetical protein (NCBI) 286, 384
PA4731 panD aspartate 1-decarboxylase precursor (NCBI) 384, 517
PA4845 dipZ thiol:disulfide interchange protein precursor (NCBI) 249, 517
PA4923 PA4923 hypothetical protein (NCBI) 255, 517
PA5302 dadX catabolic alanine racemase (NCBI) 3, 517
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 PA1490
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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