Organism : Escherichia coli K12 | Module List :
b3841

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for b3841
(Mouseover regulator name to see its description)

Warning: No Regulators were found for b3841!

Warning: b3841 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
8590 1.60e-01 tcTtTtaCgatccGtt.TtTtcac
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8591 2.60e+03 TatcCGaCgCCcgcaaTGaA
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8858 2.30e-03 gCtTtTtTTCcGTaTaCTgcccTa
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8859 3.50e+00 CcTT.cGCttTCacGgCGgtG
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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 b3841

Warning: No Functional annotations were found!

Module neighborhood information for b3841

b3841 has total of 48 gene neighbors in modules 67, 202
Gene neighbors (48)
Gene Common Name Description Module membership
NP_414648.1 hofC None 67, 196
NP_414649.1 hofB None 48, 67
NP_415087.1 ybcS None 67, 327
NP_415088.1 rzpD None 67, 91
NP_415171.1 cobC None 133, 202
NP_415173.1 holA None 202, 213
NP_415565.1 mdoC None 202, 344
NP_415614.1 pabC None 133, 202
NP_415617.1 holB None 202, 366
NP_415681.1 ycgF None 202, 210
NP_415703.3 dsbB None 202, 372
NP_415811.1 ymjA None 202, 327
NP_415873.2 ydaG None 67, 330
NP_415881.1 trkG None 148, 202
NP_415891.1 tfaR None 67, 247
NP_416075.1 cspB None 202, 344
NP_416099.1 ynfA None 67, 420
NP_416118.1 tqsA None 67, 317
NP_416157.1 anmK None 67, 292
NP_416161.4 ydhJ None 67, 167
NP_416255.1 cho None 67, 238
NP_416335.4 yebN None 67, 230
NP_416353.1 yebY None 202, 227
NP_416509.1 yeeV None 67, 303
NP_416739.1 yfaE None 35, 202
NP_416838.1 yfcR None 67, 359
NP_416841.1 yfcV None 67, 410
NP_416872.4 yfdE None 67, 126
NP_417070.2 yfiC None 171, 202
NP_417078.4 yfiP None 202, 344
NP_417084.1 yfiH None 76, 202
NP_417094.1 yfiR None 21, 202
NP_417108.4 yfjF None 202, 393
NP_417109.1 yfjG None 202, 393
NP_417175.1 yqaB None 178, 202
NP_417572.2 yqjF None 67, 325
NP_417954.1 yhiQ None 136, 202
NP_417956.1 yhiR None 136, 202
NP_418257.1 yigB None 202, 358
NP_418625.1 yjfZ None 67, 72
NP_418788.1 rsmC None 202, 347
NP_418811.2 yjjX None 202, 243
NP_418812.1 ytjC None 104, 202
YP_026262.1 rarD None 67, 354
b2612 b2612 None 171, 202
b2613 b2613 None 128, 202
b3814 b3814 None 67, 404
b3841 b3841 None 67, 202
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 b3841
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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