Organism : Pseudomonas aeruginosa | Module List :
PA4561 ribF

hypothetical protein (NCBI)

CircVis
Functional Annotations (7)
Function System
FAD synthase cog/ cog
FMN adenylyltransferase activity go/ molecular_function
riboflavin kinase activity go/ molecular_function
riboflavin biosynthetic process go/ biological_process
Riboflavin metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
ribF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4561
(Mouseover regulator name to see its description)

PA4561 is regulated by 43 influences and regulates 0 modules.
Regulators for PA4561 ribF (43)
Regulator Module Operator
PA0393 440 tf
PA0547 440 tf
PA0831 440 tf
PA1630 440 tf
PA2047 440 tf
PA2484 440 tf
PA2692 440 tf
PA3007 440 tf
PA3027 440 tf
PA3341 440 tf
PA4052 440 tf
PA4275 440 tf
PA4451 440 tf
PA4745 440 tf
PA4853 440 tf
PA4890 440 tf
PA5253 440 tf
PA5337 440 tf
PA5344 440 tf
PA5403 440 tf
PA5438 440 tf
PA0120 111 tf
PA0125 111 tf
PA0236 111 tf
PA0253 111 tf
PA0289 111 tf
PA0455 111 tf
PA0831 111 tf
PA0961 111 tf
PA1397 111 tf
PA2047 111 tf
PA2510 111 tf
PA2692 111 tf
PA2957 111 tf
PA3322 111 tf
PA3604 111 tf
PA3622 111 tf
PA4052 111 tf
PA4275 111 tf
PA4451 111 tf
PA4745 111 tf
PA4853 111 tf
PA5437 111 tf

Warning: PA4561 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
3054 1.20e-07 tAgAaTgcccgcccttTtcacc
Loader icon
3055 1.40e+04 ATaTTTA
Loader icon
3700 6.70e-02 gcTAtaAT
Loader icon
3701 4.20e+03 GTgATTcattCcG
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 PA4561

PA4561 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
FAD synthase cog/ cog
FMN adenylyltransferase activity go/ molecular_function
riboflavin kinase activity go/ molecular_function
riboflavin biosynthetic process go/ biological_process
Riboflavin metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
ribF tigr/ tigrfam
Module neighborhood information for PA4561

PA4561 has total of 24 gene neighbors in modules 111, 440
Gene neighbors (24)
Gene Common Name Description Module membership
PA0330 rpiA ribose-5-phosphate isomerase A (NCBI) 308, 440
PA0342 thyA thymidylate synthase (NCBI) 111, 398
PA0380 PA0380 sulfur carrier protein ThiS (NCBI) 111, 520
PA1299 PA1299 hypothetical protein (NCBI) 111, 230
PA1305 PA1305 hypothetical protein (NCBI) 232, 440
PA2906 PA2906 probable oxidoreductase (NCBI) 83, 440
PA3050 pyrD dihydroorotate dehydrogenase (NCBI) 111, 422
PA3665 PA3665 hypothetical protein (NCBI) 99, 440
PA3685 PA3685 hypothetical protein (NCBI) 111, 135
PA3807 ndk nucleoside diphosphate kinase (NCBI) 282, 440
PA3828 PA3828 hypothetical protein (NCBI) 111, 354
PA4004 PA4004 hypothetical protein (NCBI) 332, 440
PA4005 PA4005 hypothetical protein (NCBI) 271, 440
PA4006 nadD nicotinic acid mononucleotide adenyltransferase (NCBI) 114, 440
PA4007 proA gamma-glutamyl phosphate reductase (NCBI) 352, 440
PA4314 purU1 formyltetrahydrofolate deformylase (NCBI) 271, 440
PA4390 PA4390 hypothetical protein (NCBI) 111, 135
PA4561 ribF hypothetical protein (NCBI) 111, 440
PA4574 PA4574 hypothetical protein (NCBI) 111, 135
PA4666 hemA glutamyl-tRNA reductase (NCBI) 111, 332
PA4933 PA4933 hypothetical protein (NCBI) 440, 506
PA4940 PA4940 hypothetical protein (NCBI) 424, 440
PA5130 PA5130 hypothetical protein (NCBI) 111, 122
PA5335 PA5335 hypothetical protein (NCBI) 332, 440
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 PA4561
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