Organism : Pseudomonas aeruginosa | Module List :
PA4978

hypothetical protein (NCBI)

CircVis
Functional Annotations (3)
Function System
Acyl-CoA synthetase (NDP forming) cog/ cog
catalytic activity go/ molecular_function
ATP binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4978
(Mouseover regulator name to see its description)

PA4978 is regulated by 33 influences and regulates 0 modules.
Regulators for PA4978 (33)
Regulator Module Operator
PA0120 125 tf
PA0191 125 tf
PA0268 125 tf
PA0491 125 tf
PA1003 125 tf
PA1223 125 tf
PA1235 125 tf
PA1430 125 tf
PA1520 125 tf
PA2802 125 tf
PA3381 125 tf
PA3594 125 tf
PA3711 125 tf
PA4363 125 tf
PA4600 125 tf
PA4989 125 tf
PA5293 125 tf
PA5344 125 tf
PA0032 97 tf
PA0564 97 tf
PA0701 97 tf
PA1145 97 tf
PA1399 97 tf
PA1945 97 tf
PA2586 97 tf
PA3045 97 tf
PA3420 97 tf
PA3711 97 tf
PA4057 97 tf
PA4269 97 tf
PA5032 97 tf
PA5116 97 tf
PA5293 97 tf

Warning: PA4978 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
3026 1.40e-04 AAc.AtAagaacaAggaac
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3027 2.70e+03 tTcCaGgcAAttgtAgA
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3080 1.00e-10 ataagatcAttctAgaCAATa
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3081 1.10e-07 ACAAcaAgAaAgatg
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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 PA4978

PA4978 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Acyl-CoA synthetase (NDP forming) cog/ cog
catalytic activity go/ molecular_function
ATP binding go/ molecular_function
Module neighborhood information for PA4978

PA4978 has total of 43 gene neighbors in modules 97, 125
Gene neighbors (43)
Gene Common Name Description Module membership
PA0119 PA0119 probable dicarboxylate transporter (NCBI) 61, 125
PA0120 PA0120 probable transcriptional regulator (NCBI) 125, 441
PA0491 PA0491 probable transcriptional regulator (NCBI) 125, 526
PA0492 PA0492 hypothetical protein (NCBI) 125, 526
PA0493 PA0493 acetyl-CoA carboxylase (NCBI) 125, 526
PA0494 PA0494 acetyl-CoA carboxylase (NCBI) 125, 526
PA0495 PA0495 hypothetical protein (NCBI) 125, 526
PA0496 PA0496 hypothetical protein (NCBI) 125, 526
PA0991 PA0991 hypothetical protein (NCBI) 97, 231
PA1426 PA1426 hypothetical protein (NCBI) 97, 340
PA1451 PA1451 hypothetical protein (NCBI) 97, 245
PA1740 PA1740 hypothetical protein (NCBI) 97, 340
PA2186 PA2186 hypothetical protein (NCBI) 97, 521
PA2714 PA2714 probable molybdopterin oxidoreductase (NCBI) 97, 425
PA2845 PA2845 hypothetical protein (NCBI) 125, 333
PA2938 PA2938 probable transporter (NCBI) 97, 140
PA2984 PA2984 hypothetical protein (NCBI) 97, 190
PA4009 PA4009 hypothetical protein (NCBI) 97, 288
PA4040 PA4040 hypothetical protein (NCBI) 97, 289
PA4073 PA4073 probable aldehyde dehydrogenase (NCBI) 125, 268
PA4100 PA4100 probable dehydrogenase (NCBI) 125, 285
PA4185 PA4185 probable transcriptional regulator (NCBI) 125, 212
PA4186 PA4186 hypothetical protein (NCBI) 125, 196
PA4187 PA4187 probable major facilitator superfamily (MFS) transporter (NCBI) 125, 267
PA4188 PA4188 hypothetical protein (NCBI) 125, 267
PA4189 PA4189 probable aldehyde dehydrogenase (NCBI) 125, 267
PA4437 PA4437 hypothetical protein (NCBI) 97, 288
PA4518 PA4518 hypothetical protein (NCBI) 26, 97
PA4541 PA4541 hypothetical protein (NCBI) 97, 497
PA4597 oprJ Multidrug efflux outer membrane protein OprJ precursor (NCBI) 125, 173
PA4598 mexD Resistance-Nodulation-Cell Division (RND) multidrug efflux transporter MexD (NCBI) 125, 173
PA4599 mexC Resistance-Nodulation-Cell Division (RND) multidrug efflux membrane fusion protein MexC precursor (NCBI) 125, 173
PA4600 nfxB transcriptional regulator NfxB (NCBI) 125, 173
PA4908 PA4908 ornithine cyclodeaminase (NCBI) 74, 97
PA4975 PA4975 NAD(P)H quinone oxidoreductase (NCBI) 97, 432
PA4977 PA4977 probable acetolactate synthase large subunit (NCBI) 97, 125
PA4978 PA4978 hypothetical protein (NCBI) 97, 125
PA4979 PA4979 probable acyl-CoA dehydrogenase (NCBI) 97, 125
PA4980 PA4980 probable enoyl-CoA hydratase/isomerase (NCBI) 125, 536
PA5116 PA5116 probable transcriptional regulator (NCBI) 44, 97
PA5238 PA5238 probable O-antigen acetylase (NCBI) 97, 498
PA5476 citA citrate transporter (NCBI) 16, 97
PA5530 PA5530 probable MFS dicarboxylate transporter (NCBI) 23, 125
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 PA4978
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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