Organism : Pseudomonas aeruginosa | Module List :
PA0161

hypothetical protein (NCBI)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0161
(Mouseover regulator name to see its description)

PA0161 is regulated by 30 influences and regulates 0 modules.
Regulators for PA0161 (30)
Regulator Module Operator
PA0032 23 tf
PA0163 23 tf
PA0564 23 tf
PA0701 23 tf
PA1136 23 tf
PA1998 23 tf
PA3381 23 tf
PA4989 23 tf
PA5525 23 tf
PA0225 231 tf
PA0701 231 tf
PA0979 231 tf
PA1067 231 tf
PA1142 231 tf
PA2076 231 tf
PA2220 231 tf
PA2227 231 tf
PA2383 231 tf
PA2736 231 tf
PA3045 231 tf
PA3215 231 tf
PA3364 231 tf
PA3757 231 tf
PA3879 231 tf
PA3948 231 tf
PA4077 231 tf
PA4080 231 tf
PA4269 231 tf
PA4436 231 tf
PA5438 231 tf

Warning: PA0161 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
2882 1.60e-05 gAaAat.tcgttaaaaCat.A
Loader icon
2883 2.10e-05 CGCCTgcC.AgcCTG
Loader icon
3290 2.40e-06 ActaTctaaaaCacga.cag
Loader icon
3291 1.50e-02 aaAaAta.cat
Loader icon
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 PA0161

Warning: No Functional annotations were found!

Module neighborhood information for PA0161

PA0161 has total of 53 gene neighbors in modules 23, 231
Gene neighbors (53)
Gene Common Name Description Module membership
PA0014 PA0014 hypothetical protein (NCBI) 23, 498
PA0161 PA0161 hypothetical protein (NCBI) 23, 231
PA0486 PA0486 hypothetical protein (NCBI) 23, 101
PA0497 PA0497 hypothetical protein (NCBI) 231, 324
PA0498 PA0498 hypothetical protein (NCBI) 231, 324
PA0499 PA0499 probable pili assembly chaperone (NCBI) 231, 326
PA0531 PA0531 probable glutamine amidotransferase (NCBI) 23, 536
PA0568 PA0568 hypothetical protein (NCBI) 23, 189
PA0570 PA0570 hypothetical protein (NCBI) 23, 189
PA0702 PA0702 hypothetical protein (NCBI) 23, 408
PA0806 PA0806 hypothetical protein (NCBI) 23, 330
PA0821 PA0821 hypothetical protein (NCBI) 157, 231
PA0822 PA0822 hypothetical protein (NCBI) 157, 231
PA0826 PA0826 hypothetical protein (NCBI) 188, 231
PA0978 PA0978 hypothetical protein (NCBI) 61, 231
PA0979 PA0979 hypothetical protein (NCBI) 231, 338
PA0980 PA0980 hypothetical protein (NCBI) 188, 231
PA0981 PA0981 hypothetical protein (NCBI) 231, 385
PA0984 PA0984 colicin immunity protein (NCBI) 101, 231
PA0991 PA0991 hypothetical protein (NCBI) 97, 231
PA0992 cupC1 fimbrial subunit CupC1 (NCBI) 231, 385
PA0994 cupC3 usher CupC3 (NCBI) 71, 231
PA1107 PA1107 hypothetical protein (NCBI) 23, 537
PA1152 PA1152 hypothetical protein (NCBI) 188, 231
PA1321 cyoE cytochrome o ubiquinol oxidase protein CyoE (NCBI) 23, 335
PA1424 PA1424 hypothetical protein (NCBI) 23, 335
PA1755 PA1755 hypothetical protein (NCBI) 23, 550
PA2036 PA2036 hypothetical protein (NCBI) 231, 445
PA2037 PA2037 hypothetical protein (NCBI) 188, 231
PA2125 PA2125 probable aldehyde dehydrogenase (NCBI) 23, 507
PA2730 PA2730 hypothetical protein (NCBI) 231, 485
PA2913 PA2913 hypothetical protein (NCBI) 23, 83
PA2929 PA2929 hypothetical protein (NCBI) 23, 101
PA3153 wzx O-antigen translocase (NCBI) 231, 485
PA3497 PA3497 hypothetical protein (NCBI) 80, 231
PA4062 PA4062 hypothetical protein (NCBI) 23, 236
PA4063 PA4063 hypothetical protein (NCBI) 23, 134
PA4064 PA4064 probable ATP-binding component of ABC transporter (NCBI) 23, 134
PA4065 PA4065 hypothetical protein (NCBI) 23, 134
PA4066 PA4066 hypothetical protein (NCBI) 23, 134
PA4349 PA4349 hypothetical protein (NCBI) 23, 475
PA4351 PA4351 probable acyltransferase (NCBI) 23, 192
PA4834 PA4834 hypothetical protein (NCBI) 23, 134
PA4871 PA4871 hypothetical protein (NCBI) 23, 311
PA4962 PA4962 hypothetical protein (NCBI) 23, 377
PA4990 PA4990 SMR multidrug efflux transporter (NCBI) 23, 266
PA4999 waaL O-antigen ligase, WaaL (NCBI) 231, 375
PA5086 PA5086 hypothetical protein (NCBI) 231, 321
PA5087 PA5087 hypothetical protein (NCBI) 231, 473
PA5088 PA5088 hypothetical protein (NCBI) 231, 324
PA5264 PA5264 hypothetical protein (NCBI) 188, 231
PA5530 PA5530 probable MFS dicarboxylate transporter (NCBI) 23, 125
PA5532 PA5532 hypothetical protein (NCBI) 23, 445
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 PA0161
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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