Organism : Escherichia coli K12 | Module List :
b2858 ygeN

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for b2858
(Mouseover regulator name to see its description)

Warning: No Regulators were found for b2858!

Warning: b2858 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
8966 8.50e-04 TccaTT.tCgCctTcCtTca.g.C
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8967 5.70e+01 cgTTgtGaaa.AtcatGctagcGc
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9082 3.50e-03 taagCCgcAttattt.tg.GGttA
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9083 9.80e+00 GcAAAgcGgcatGCA
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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 b2858

Warning: No Functional annotations were found!

Module neighborhood information for b2858

b2858 has total of 48 gene neighbors in modules 257, 316
Gene neighbors (48)
Gene Common Name Description Module membership
NP_414622.1 fruR None 316, 377
NP_414746.1 yafE None 316, 377
NP_414980.2 cof None 198, 316
NP_414988.1 ybaZ None 257, 316
NP_415015.1 ybaP None 257, 380
NP_415016.4 ybaQ None 249, 257
NP_415111.1 ybdF None 257, 327
NP_415133.1 ybdL None 2, 257
NP_415284.1 modA None 2, 316
NP_415285.1 modB None 316, 377
NP_415286.1 modC None 2, 316
NP_415292.2 ybhJ None 82, 257
NP_415319.1 ybiA None 2, 316
NP_415320.1 dinG None 316, 333
NP_415323.1 ybiJ None 41, 257
NP_415429.2 ycaL None 2, 257
NP_415466.4 ycbW None 171, 257
NP_415476.1 ycbG None 45, 257
NP_415502.4 etp None 257, 360
NP_415510.1 cspG None 257, 344
NP_415511.1 ymcE None 257, 341
NP_415513.2 torS None 222, 316
NP_415514.1 torT None 10, 316
NP_415515.1 torR None 2, 316
NP_415540.1 pgaD None 257, 283
NP_415541.1 pgaC None 257, 360
NP_415581.1 yceB None 257, 351
NP_415698.1 ycgM None 198, 257
NP_415795.1 yciS None 95, 316
NP_416067.2 ydfO None 199, 257
NP_416285.1 ydjG None 231, 316
NP_416287.1 ydjI None 53, 316
NP_416289.1 ydjK None 231, 316
NP_416295.1 yeaE None 316, 409
NP_416387.1 torY None 2, 257
NP_416389.4 yecM None 84, 316
NP_416569.1 dcd None 276, 316
NP_416835.2 yfcO None 249, 316
NP_417056.2 yfhH None 41, 316
NP_417153.1 ygaV None 257, 279
NP_417154.1 ygaP None 257, 413
NP_417235.1 ygbT None 316, 410
NP_417294.4 amiC None 54, 316
NP_417531.1 ygiH None 284, 316
NP_418503.1 fdhF None 316, 341
YP_025309.2 cutC None 92, 316
b1028 ymdE None 19, 257
b2858 ygeN None 257, 316
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 b2858
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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