Organism : Escherichia coli K12 | Module List :
YP_025302.1 uxaB

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for YP_025302.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for YP_025302.1!

Warning: YP_025302.1 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
8782 5.50e+03 CCaTatcaaATGGctGGttAaA
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8783 3.90e+04 AC.TCGgGCGT
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8952 6.30e+01 aAatGAtaTaCgT.gCGcaaa
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8953 1.10e+02 TTgTgTaAcaA
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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 YP_025302.1

Warning: No Functional annotations were found!

Module neighborhood information for YP_025302.1

YP_025302.1 has total of 44 gene neighbors in modules 163, 250
Gene neighbors (44)
Gene Common Name Description Module membership
NP_414606.1 araC None 250, 298
NP_414687.1 dksA None 250, 261
NP_414704.4 cdaR None 215, 250
NP_414840.1 ykgE None 2, 250
NP_414841.1 ykgF None 110, 250
NP_414842.4 ykgG None 110, 250
NP_414844.1 ykgH None 39, 163
NP_414914.2 yaiZ None 185, 250
NP_414916.1 iraP None 233, 250
NP_414933.1 phoB None 175, 250
NP_414934.1 phoR None 215, 250
NP_415143.1 rnk None 188, 250
NP_415366.1 ybjJ None 129, 250
NP_415367.1 ybjK None 129, 250
NP_415603.2 yceQ None 250, 309
NP_415699.5 ycgN None 250, 417
NP_415855.1 abgR None 250, 273
NP_415861.1 intR None 119, 163
NP_415916.1 paaK None 250, 286
NP_415929.1 ynbD None 53, 163
NP_415950.4 ydcO None 25, 163
NP_415959.1 ydcU None 250, 272
NP_415961.1 ydcW None 250, 356
NP_416112.1 ynfL None 163, 173
NP_416212.1 ydiQ None 45, 163
NP_416319.1 fadD None 250, 332
NP_416469.1 vsr None 163, 198
NP_416579.1 mdtB None 78, 163
NP_416582.1 baeS None 2, 163
NP_416732.4 yfaT None 53, 163
NP_416736.1 yfaL None 147, 163
NP_416836.1 yfcP None 20, 163
NP_416839.1 yfcS None 44, 163
NP_416846.2 fadL None 250, 332
NP_417031.1 hcaT None 78, 250
NP_417241.1 ygcB None 44, 163
NP_417308.1 mutH None 163, 280
NP_417321.2 yqeF None 129, 250
NP_417451.1 glcG None 77, 250
NP_417453.1 glcD None 29, 250
NP_417606.1 kbaY None 163, 181
NP_418483.1 ssb None 250, 261
YP_025302.1 uxaB None 163, 250
b3435 b3435 None 163, 230
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_025302.1
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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