Organism : Pseudomonas aeruginosa | Module List :
PA0645

hypothetical protein (NCBI)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0645
(Mouseover regulator name to see its description)

PA0645 is regulated by 57 influences and regulates 0 modules.
Regulators for PA0645 (57)
Regulator Module Operator
PA0233 188 tf
PA0535 188 tf
PA0791 188 tf
PA0873 188 tf
PA1229 188 tf
PA1261 188 tf
PA1359 188 tf
PA1363 188 tf
PA2054 188 tf
PA2076 188 tf
PA2227 188 tf
PA2376 188 tf
PA2736 188 tf
PA3045 188 tf
PA3699 188 tf
PA3711 188 tf
PA3757 188 tf
PA3879 188 tf
PA4077 188 tf
PA4269 188 tf
PA5337 188 tf
PA5438 188 tf
PA0268 297 tf
PA0393 297 tf
PA0455 297 tf
PA0611 297 tf
PA0784 297 tf
PA0815 297 tf
PA0890 297 tf
PA1141 297 tf
PA1226 297 tf
PA1229 297 tf
PA1290 297 tf
PA1328 297 tf
PA1363 297 tf
PA1619 297 tf
PA1630 297 tf
PA1633 297 tf
PA1663 297 tf
PA2047 297 tf
PA2054 297 tf
PA2100 297 tf
PA2126 297 tf
PA2196 297 tf
PA2227 297 tf
PA2387 297 tf
PA2692 297 tf
PA2718 297 tf
PA2736 297 tf
PA2758 297 tf
PA2849 297 tf
PA3067 297 tf
PA3215 297 tf
PA3711 297 tf
PA3815 297 tf
PA3898 297 tf
PA3995 297 tf

Warning: PA0645 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
3204 1.80e-06 atTccaAAAtaagata.tt
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3205 2.60e-02 a.aaAttgAct.TtA
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3422 3.90e-07 Tta.tAaacta.gtTTTCaaa
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3423 6.00e+00 aATAA.gAAgt
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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 PA0645

Warning: No Functional annotations were found!

Module neighborhood information for PA0645

PA0645 has total of 36 gene neighbors in modules 188, 297
Gene neighbors (36)
Gene Common Name Description Module membership
PA0053 PA0053 hypothetical protein (NCBI) 297, 476
PA0642 PA0642 hypothetical protein (NCBI) 11, 188
PA0643 PA0643 hypothetical protein (NCBI) 188, 297
PA0644 PA0644 hypothetical protein (NCBI) 188, 297
PA0645 PA0645 hypothetical protein (NCBI) 188, 297
PA0646 PA0646 hypothetical protein (NCBI) 11, 188
PA0647 PA0647 hypothetical protein (NCBI) 11, 188
PA0715 PA0715 hypothetical protein (NCBI) 188, 485
PA0716 PA0716 hypothetical protein (NCBI) 188, 485
PA0729 PA0729 hypothetical protein (NCBI) 168, 297
PA0826 PA0826 hypothetical protein (NCBI) 188, 231
PA0980 PA0980 hypothetical protein (NCBI) 188, 231
PA1150 pys2 pyocin S2 (NCBI) 11, 297
PA1151 imm2 pyocin S2 immunity protein (NCBI) 11, 297
PA1152 PA1152 hypothetical protein (NCBI) 188, 231
PA1366 PA1366 hypothetical protein (NCBI) 297, 476
PA1371 PA1371 hypothetical protein (NCBI) 188, 476
PA1372 PA1372 hypothetical protein (NCBI) 297, 476
PA2037 PA2037 hypothetical protein (NCBI) 188, 231
PA2222 PA2222 hypothetical protein (NCBI) 188, 476
PA2223 PA2223 hypothetical protein (NCBI) 188, 476
PA2224 PA2224 hypothetical protein (NCBI) 188, 385
PA2225 PA2225 hypothetical protein (NCBI) 188, 385
PA2226 PA2226 hypothetical protein (NCBI) 188, 385
PA2227 PA2227 probable transcriptional regulator (NCBI) 188, 385
PA2228 PA2228 hypothetical protein (NCBI) 188, 385
PA2462 PA2462 hypothetical protein (NCBI) 62, 297
PA2794 PA2794 hypothetical protein (NCBI) 152, 188
PA3142 PA3142 hypothetical protein (NCBI) 297, 476
PA3143 PA3143 hypothetical protein (NCBI) 297, 476
PA3144 PA3144 hypothetical protein (NCBI) 219, 297
PA3157 PA3157 probable acetyltransferase (NCBI) 297, 476
PA3158 wbpB probable oxidoreductase WpbB (NCBI) 219, 297
PA3159 wbpA probable UDP-glucose/GDP-mannose dehydrogenase WbpA (NCBI) 219, 297
PA3160 wzz O-antigen chain length regulator (NCBI) 297, 476
PA5264 PA5264 hypothetical protein (NCBI) 188, 231
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 PA0645
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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