Organism : Escherichia coli K12 | Module List :
b2613

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for b2613
(Mouseover regulator name to see its description)

Warning: No Regulators were found for b2613!

Warning: b2613 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
8712 1.80e-02 CTtcATGTTAaAcaaCGGcAAAA
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8713 6.90e-02 cGGcGCAGaGTttAc
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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 b2613

Warning: No Functional annotations were found!

Module neighborhood information for b2613

b2613 has total of 46 gene neighbors in modules 128, 202
Gene neighbors (46)
Gene Common Name Description Module membership
NP_414699.1 yadS None 106, 128
NP_414759.1 yafK None 128, 329
NP_414967.1 ampG None 106, 128
NP_415002.1 apt None 128, 138
NP_415003.1 dnaX None 97, 128
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_415634.1 lolC None 128, 378
NP_415635.4 lolD None 128, 209
NP_415681.1 ycgF None 202, 210
NP_415703.3 dsbB None 202, 372
NP_415811.1 ymjA None 202, 327
NP_415881.1 trkG None 148, 202
NP_416040.1 yneG None 128, 218
NP_416041.1 yneH None 128, 366
NP_416075.1 cspB None 202, 344
NP_416300.2 yeaJ None 125, 128
NP_416336.1 rrmA None 128, 327
NP_416353.1 yebY None 202, 227
NP_416739.1 yfaE None 35, 202
NP_416991.1 hda None 96, 128
NP_417027.1 trmJ None 128, 343
NP_417028.1 suhB None 128, 277
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_417101.1 ffh None 117, 128
NP_417102.4 ypjD None 117, 128
NP_417108.4 yfjF None 202, 393
NP_417109.1 yfjG None 202, 393
NP_417170.1 emrA None 62, 128
NP_417175.1 yqaB None 178, 202
NP_417954.1 yhiQ None 136, 202
NP_417956.1 yhiR None 136, 202
NP_418257.1 yigB None 202, 358
NP_418416.1 yjaZ None 128, 329
NP_418788.1 rsmC None 202, 347
NP_418811.2 yjjX None 202, 243
NP_418812.1 ytjC None 104, 202
b2612 b2612 None 171, 202
b2613 b2613 None 128, 202
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 b2613
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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