Organism : Escherichia coli K12 | Module List :
YP_026278.1 ptsA

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for YP_026278.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for YP_026278.1!

Warning: YP_026278.1 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
8474 2.00e+03 CggcTGaaAatTT.aCcccGg
Loader icon
8475 2.30e+04 gA.AgcggctT.cgcaa.cCg.g
Loader icon
8842 2.10e+02 AcCcgCAgaatGcga
Loader icon
8843 2.10e+03 tGa.gaa.AgCtggcg.Aagccgc
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 YP_026278.1

Warning: No Functional annotations were found!

Module neighborhood information for YP_026278.1

YP_026278.1 has total of 44 gene neighbors in modules 8, 194
Gene neighbors (44)
Gene Common Name Description Module membership
NP_414587.1 yaaU None 194, 196
NP_415091.1 ybcW None 194, 221
NP_415355.1 yliF None 28, 194
NP_415393.1 hcr None 153, 194
NP_415394.4 hcp None 153, 194
NP_415836.1 ycjW None 194, 399
NP_415865.1 recT None 28, 194
NP_416269.4 ynjC None 137, 194
NP_416273.1 nudG None 194, 228
NP_416603.1 yegV None 8, 201
NP_416963.1 aegA None 194, 320
NP_417036.1 hcaB None 28, 194
NP_417040.2 yphC None 12, 194
NP_417049.1 yfhA None 8, 314
NP_417203.1 hycC None 81, 194
NP_417216.1 ygbJ None 8, 352
NP_417256.1 ygcE None 137, 194
NP_417623.1 yhbP None 8, 205
NP_417723.1 yhdT None 8, 228
NP_417728.4 yhdJ None 8, 194
NP_417836.1 yhfT None 8, 55
NP_417838.1 php None 8, 12
NP_417870.1 yhgA None 8, 120
NP_418006.1 yiaC None 8, 88
NP_418110.1 gltS None 8, 420
NP_418209.1 rbsR None 8, 134
NP_418241.1 wzyE None 8, 228
NP_418242.1 rffM None 8, 228
NP_418384.1 frwC None 8, 194
NP_418385.1 frwB None 8, 326
NP_418388.1 frwD None 194, 368
NP_418430.2 zraP None 101, 194
NP_418468.3 dinF None 8, 371
NP_418604.1 yjfK None 12, 194
NP_418605.1 yjfL None 12, 194
NP_418606.1 yjfM None 12, 194
NP_418607.1 yjfC None 194, 205
NP_418686.1 idnT None 8, 298
NP_418716.1 yjhF None 8, 103
YP_026278.1 ptsA None 8, 194
YP_026285.1 ytfI None 8, 301
b0322 b0322 None 8, 303
b2885 b2885 None 8, 10
b4103 b4103 None 154, 194
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 YP_026278.1
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