Organism : Escherichia coli K12 | Module List :
b4236 cybC

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for b4236
(Mouseover regulator name to see its description)

Warning: No Regulators were found for b4236!

Warning: b4236 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
8546 3.40e+03 taTtgtT.a.aaAatg.a.ttaA
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8547 6.50e+04 ccCCGcaCcGc
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8958 2.70e+04 taAcgcTgAAA
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8959 1.30e+04 TcAtcG.TTaca.AAAaATttATc
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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 b4236

Warning: No Functional annotations were found!

Module neighborhood information for b4236

b4236 has total of 56 gene neighbors in modules 45, 253
Gene neighbors (56)
Gene Common Name Description Module membership
NP_414706.2 yaeI None 45, 131
NP_414745.1 yafD None 45, 174
NP_414822.1 ykgJ None 45, 133
NP_414945.1 tsx None 178, 253
NP_414998.1 kefA None 45, 327
NP_415096.1 appY None 17, 45
NP_415474.1 fabA None 178, 253
NP_415476.1 ycbG None 45, 257
NP_415478.1 sulA None 45, 387
NP_415533.1 rutR None 45, 201
NP_415663.1 ymfK None 45, 351
NP_415844.1 ycjZ None 45, 339
NP_415931.4 hrpA None 78, 253
NP_415946.1 tehA None 45, 407
NP_415996.2 maeA None 117, 253
NP_416060.1 ydfI None 45, 360
NP_416090.2 ydfB None 45, 271
NP_416159.2 slyA None 45, 232
NP_416212.1 ydiQ None 45, 163
NP_416617.1 metG None 253, 277
NP_416686.1 yejG None 45, 255
NP_416775.1 yfbM None 45, 222
NP_416903.1 yfeN None 45, 322
NP_416905.1 yfeH None 45, 188
NP_417047.1 hmp None 45, 110
NP_417071.1 srmB None 138, 253
NP_417077.1 trxC None 45, 255
NP_417213.1 mutS None 218, 253
NP_417276.1 sdaC None 253, 336
NP_417277.1 sdaB None 230, 253
NP_417319.1 kduD None 45, 368
NP_417412.1 speB None 140, 253
NP_417413.1 speA None 253, 363
NP_417418.1 galP None 214, 253
NP_417427.1 yggT None 253, 391
NP_417429.1 rdgB None 100, 253
NP_417501.1 ygiN None 45, 232
NP_417539.1 rpoD None 50, 253
NP_417561.1 ygjV None 43, 45
NP_417565.2 exuR None 45, 243
NP_417620.1 yraQ None 91, 253
NP_417704.1 argR None 157, 253
NP_418064.1 cysE None 253, 307
NP_418185.1 glmS None 74, 253
NP_418265.1 pldA None 253, 277
NP_418347.1 cpxA None 1, 253
NP_418368.1 ftsN None 244, 253
NP_418369.1 cytR None 253, 303
NP_418415.1 rpoC None 106, 253
NP_418487.1 soxR None 10, 45
NP_418533.1 yjdA None 45, 114
NP_418598.1 purA None 253, 304
NP_418685.1 idnR None 45, 70
b0263 afuB None 45, 330
b4236 cybC None 45, 253
b4285 b4285 None 43, 45
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 b4236
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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