Organism : Pseudomonas aeruginosa | Module List :
PA0550

hypothetical protein (NCBI)

CircVis
Functional Annotations (4)
Function System
Hydroxypyruvate isomerase cog/ cog
hydroxypyruvate isomerase activity go/ molecular_function
Glyoxylate and dicarboxylate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0550
(Mouseover regulator name to see its description)

PA0550 is regulated by 43 influences and regulates 0 modules.
Regulators for PA0550 (43)
Regulator Module Operator
PA0217 175 tf
PA0448 175 tf
PA0564 175 tf
PA1128 175 tf
PA1261 175 tf
PA1526 175 tf
PA2050 175 tf
PA2917 175 tf
PA3249 175 tf
PA3711 175 tf
PA3757 175 tf
PA3830 175 tf
PA4169 175 tf
PA4174 175 tf
PA5032 175 tf
PA0167 420 tf
PA0393 420 tf
PA0436 420 tf
PA0611 420 tf
PA0839 420 tf
PA0890 420 tf
PA1136 420 tf
PA1539 420 tf
PA1859 420 tf
PA1864 420 tf
PA2054 420 tf
PA2320 420 tf
PA2825 420 tf
PA2849 420 tf
PA2897 420 tf
PA3002 420 tf
PA3027 420 tf
PA3714 420 tf
PA3927 420 tf
PA4052 420 tf
PA4057 420 tf
PA4238 420 tf
PA4269 420 tf
PA4596 420 tf
PA4755 420 tf
PA5253 420 tf
PA5342 420 tf
PA5344 420 tf

Warning: PA0550 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
3178 3.80e+02 AtcGgGaaAA
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3179 6.00e+04 AAGTGTCATT
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3662 2.00e+03 AGGaAAAAcGc
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3663 1.90e+04 AgGAAatC
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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 PA0550

PA0550 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Hydroxypyruvate isomerase cog/ cog
hydroxypyruvate isomerase activity go/ molecular_function
Glyoxylate and dicarboxylate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for PA0550

PA0550 has total of 51 gene neighbors in modules 175, 420
Gene neighbors (51)
Gene Common Name Description Module membership
PA0142 PA0142 hydroxydechloroatrazine ethylaminohydrolase (NCBI) 175, 192
PA0223 PA0223 probable dihydrodipicolinate synthetase (NCBI) 175, 489
PA0353 ilvD dihydroxy-acid dehydratase (NCBI) 42, 420
PA0421 PA0421 hypothetical protein (NCBI) 78, 420
PA0448 PA0448 probable transcriptional regulator (NCBI) 175, 438
PA0550 PA0550 hypothetical protein (NCBI) 175, 420
PA0600 PA0600 probable two-component sensor (NCBI) 175, 245
PA0651 trpC indole-3-glycerol-phosphate synthase (NCBI) 8, 420
PA0934 relA GTP pyrophosphokinase (NCBI) 420, 462
PA1047 PA1047 probable esterase (NCBI) 220, 420
PA1113 PA1113 probable ATP-binding/permease fusion ABC transporter (NCBI) 175, 537
PA1128 PA1128 probable transcriptional regulator (NCBI) 175, 438
PA1158 PA1158 probable two-component sensor (NCBI) 175, 528
PA1171 PA1171 probable transglycolase (NCBI) 268, 420
PA1334 PA1334 probable oxidoreductase (NCBI) 175, 333
PA1406 PA1406 hypothetical protein (NCBI) 175, 372
PA1646 PA1646 probable chemotaxis transducer (NCBI) 175, 345
PA1820 nhaB sodium/proton antiporter NhaB (NCBI) 175, 478
PA1825 PA1825 hypothetical protein (NCBI) 33, 175
PA1906 PA1906 hypothetical protein (NCBI) 175, 489
PA2521 czcB Resistance-Nodulation-Cell Division (RND) divalent metal cation efflux membrane fusion protein CzcB precursor (NCBI) 175, 446
PA2688 pfeA Ferric enterobactin receptor, outer membrane protein PfeA precursor (NCBI) 175, 339
PA2917 PA2917 probable transcriptional regulator (NCBI) 175, 333
PA3028 moeA2 molybdenum cofactor biosynthesis protein A2 (NCBI) 420, 540
PA3206 PA3206 probable two-component sensor (NCBI) 175, 313
PA3313 PA3313 hypothetical protein (NCBI) 234, 420
PA3314 PA3314 probable ATP-binding component of ABC transporter (NCBI) 420, 478
PA3357 dsdA D-serine dehydratase (NCBI) 420, 524
PA3464 PA3464 hypothetical protein (NCBI) 175, 192
PA3481 PA3481 hypothetical protein (NCBI) 420, 540
PA3605 PA3605 hypothetical protein (NCBI) 175, 247
PA3674 PA3674 hypothetical protein (NCBI) 238, 420
PA3733 PA3733 hypothetical protein (NCBI) 175, 192
PA3749 PA3749 probable major facilitator superfamily (MFS) transporter (NCBI) 175, 337
PA3783 PA3783 hypothetical protein (NCBI) 175, 241
PA3830 PA3830 probable transcriptional regulator (NCBI) 33, 175
PA3927 PA3927 probable transcriptional regulator (NCBI) 33, 175
PA3960 PA3960 hypothetical protein (NCBI) 175, 408
PA4082 cupB5 adhesive protein CupB5 (NCBI) 175, 192
PA4146 PA4146 hypothetical protein (NCBI) 175, 536
PA4167 PA4167 probable oxidoreductase (NCBI) 175, 266
PA4655 hemH ferrochelatase (NCBI) 420, 477
PA4689 PA4689 hypothetical protein (NCBI) 420, 493
PA4715 PA4715 hypothetical protein (NCBI) 91, 420
PA4804 PA4804 probable amino acid permease (NCBI) 175, 267
PA4907 PA4907 probable short-chain dehydrogenase (NCBI) 42, 420
PA5079 PA5079 D-tyrosyl-tRNA deacylase (NCBI) 420, 462
PA5146 PA5146 hypothetical protein (NCBI) 420, 435
PA5214 gcvH1 glycine cleavage system protein H1 (NCBI) 42, 420
PA5292 pchP phosphorylcholine phosphatase (NCBI) 175, 292
PA5413 ltaA low specificity l-threonine aldolase (NCBI) 293, 420
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 PA0550
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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