Organism : Pseudomonas aeruginosa | Module List :
PA3916 moaE

molybdopterin converting factor, large subunit (NCBI)

CircVis
Functional Annotations (3)
Function System
Molybdopterin converting factor, large subunit cog/ cog
Mo-molybdopterin cofactor biosynthetic process go/ biological_process
Sulfur relay system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3916
(Mouseover regulator name to see its description)

PA3916 is regulated by 35 influences and regulates 0 modules.
Regulators for PA3916 moaE (35)
Regulator Module Operator
PA0424 212 tf
PA0535 212 tf
PA1754 212 tf
PA2047 212 tf
PA3006 212 tf
PA3948 212 tf
PA3965 212 tf
PA4185 212 tf
PA4275 212 tf
PA4451 212 tf
PA4600 212 tf
PA4906 212 tf
PA5239 212 tf
PA5308 212 tf
PA5337 212 tf
PA5438 212 tf
PA0610 376 tf
PA0763 376 tf
PA0784 376 tf
PA0815 376 tf
PA0942 376 tf
PA1283 376 tf
PA1754 376 tf
PA2849 376 tf
PA2897 376 tf
PA3007 376 tf
PA3587 376 tf
PA3689 376 tf
PA3973 376 tf
PA4787 376 tf
PA4878 376 tf
PA5253 376 tf
PA5308 376 tf
PA5374 376 tf
PA5438 376 tf

Warning: PA3916 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
3252 6.30e+00 ACaTAAAA
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3253 7.00e-02 TGtaaaTaTaTT
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3576 1.70e-01 ttT.tTGtAtACAa
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3577 1.30e+03 AGCAAtaT
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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 PA3916

PA3916 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Molybdopterin converting factor, large subunit cog/ cog
Mo-molybdopterin cofactor biosynthetic process go/ biological_process
Sulfur relay system kegg/ kegg pathway
Module neighborhood information for PA3916

PA3916 has total of 49 gene neighbors in modules 212, 376
Gene neighbors (49)
Gene Common Name Description Module membership
PA0320 PA0320 hypothetical protein (NCBI) 9, 212
PA0377 PA0377 hypothetical protein (NCBI) 212, 341
PA0469 PA0469 hypothetical protein (NCBI) 376, 457
PA0534 PA0534 hypothetical protein (NCBI) 152, 212
PA0535 PA0535 probable transcriptional regulator (NCBI) 152, 212
PA0653 PA0653 hypothetical protein (NCBI) 212, 499
PA0730 PA0730 probable transferase (NCBI) 212, 371
PA0936 lpxO2 lipopolysaccharide biosynthetic protein LpxO2 (NCBI) 86, 212
PA1029 PA1029 hypothetical protein (NCBI) 376, 460
PA1030 PA1030 hypothetical protein (NCBI) 376, 460
PA1035 PA1035 hypothetical protein (NCBI) 212, 271
PA1053 PA1053 hypothetical protein (NCBI) 88, 376
PA1183 dctA C4-dicarboxylate transport protein (NCBI) 166, 212
PA1517 PA1517 hypothetical protein (NCBI) 243, 376
PA1518 PA1518 hypothetical protein (NCBI) 243, 376
PA1572 PA1572 hypothetical protein (NCBI) 361, 376
PA1573 PA1573 hypothetical protein (NCBI) 166, 376
PA1608 PA1608 probable chemotaxis transducer (NCBI) 212, 268
PA1677 PA1677 hypothetical protein (NCBI) 2, 376
PA2020 PA2020 probable transcriptional regulator (NCBI) 212, 309
PA2604 PA2604 hypothetical protein (NCBI) 376, 524
PA2769 PA2769 hypothetical protein (NCBI) 126, 212
PA2826 PA2826 probable glutathione peroxidase (NCBI) 79, 376
PA2827 PA2827 methionine sulfoxide reductase B (NCBI) 205, 376
PA2897 PA2897 probable transcriptional regulator (NCBI) 63, 376
PA3017 PA3017 hypothetical protein (NCBI) 63, 376
PA3240 PA3240 hypothetical protein (NCBI) 39, 212
PA3306 PA3306 hypothetical protein (NCBI) 63, 376
PA3721 PA3721 probable transcriptional regulator (NCBI) 189, 212
PA3730 PA3730 hypothetical protein (NCBI) 212, 468
PA3731 PA3731 hypothetical protein (NCBI) 376, 468
PA3732 PA3732 hypothetical protein (NCBI) 376, 468
PA3865 PA3865 probable amino acid binding protein (NCBI) 79, 376
PA3866 PA3866 pyocin protein (NCBI) 11, 212
PA3916 moaE molybdopterin converting factor, large subunit (NCBI) 212, 376
PA3917 moaD molybdopterin converting factor, small subunit (NCBI) 212, 376
PA3918 moaC molybdenum cofactor biosynthesis protein C (NCBI) 212, 376
PA3948 PA3948 probable two-component response regulator (NCBI) 212, 477
PA3951 PA3951 hypothetical protein (NCBI) 212, 306
PA4185 PA4185 probable transcriptional regulator (NCBI) 125, 212
PA4405 PA4405 hypothetical protein (NCBI) 212, 511
PA4427 sspB stringent starvation protein B (NCBI) 131, 212
PA4499 PA4499 probable transcriptional regulator (NCBI) 131, 212
PA4596 PA4596 probable transcriptional regulator (NCBI) 212, 550
PA5157 PA5157 probable transcriptional regulator (NCBI) 212, 473
PA5330 PA5330 hypothetical protein (NCBI) 212, 352
PA5350 rubA2 rubredoxin 2 (NCBI) 212, 338
PA5446 PA5446 hypothetical protein (NCBI) 224, 376
PA5527 PA5527 hypothetical protein (NCBI) 212, 224
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 PA3916
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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