Organism : Escherichia coli K12 | Module List :
b2640

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for b2640
(Mouseover regulator name to see its description)

Warning: No Regulators were found for b2640!

Warning: b2640 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
8542 1.90e+03 CaaTa.gCtGtagTGaTaAAaC
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8543 1.10e+04 gCCggCCtgGC
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8600 7.00e-03 CcaTTGTTcTCaTTTGacTTACAA
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8601 1.10e+03 TgaAcATtct.tAatAaTacCGcg
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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 b2640

Warning: No Functional annotations were found!

Module neighborhood information for b2640

b2640 has total of 57 gene neighbors in modules 43, 72
Gene neighbors (57)
Gene Common Name Description Module membership
NP_414775.1 crl None 43, 255
NP_415338.1 mntR None 43, 255
NP_415368.1 ybjL None 41, 43
NP_415379.1 ybjO None 43, 78
NP_415434.1 msbA None 43, 379
NP_415435.1 lpxK None 43, 408
NP_415586.1 yceM None 43, 92
NP_415712.1 ycgR None 43, 186
NP_415725.1 prs None 18, 43
NP_416404.1 motA None 43, 186
NP_417029.3 yfhR None 43, 280
NP_417124.4 yfjS None 72, 248
NP_417125.1 yfjT None 72, 248
NP_417163.1 proV None 43, 70
NP_417420.1 endA None 43, 303
NP_417458.1 yghR None 72, 305
NP_417459.1 yghS None 72, 306
NP_417472.1 yghW None 43, 352
NP_417555.4 rlmG None 72, 305
NP_417561.1 ygjV None 43, 45
NP_417871.1 bioH None 72, 91
NP_417872.2 gntX None 72, 104
NP_417892.1 yhgN None 42, 43
NP_417942.5 yhhJ None 72, 305
NP_417944.1 yhiI None 43, 134
NP_417949.1 yhiN None 72, 140
NP_417978.2 yhjC None 72, 373
NP_417982.2 yhjH None 43, 405
NP_417984.1 yhjJ None 43, 338
NP_418018.1 wecH None 43, 159
NP_418113.1 yicI None 72, 359
NP_418115.1 setC None 72, 305
NP_418120.2 yicO None 72, 305
NP_418121.1 ade None 72, 305
NP_418125.1 uhpA None 43, 54
NP_418186.1 glmU None 43, 303
NP_418294.1 mobA None 43, 302
NP_418429.1 yjaH None 72, 189
NP_418463.4 ubiC None 43, 91
NP_418464.1 ubiA None 43, 104
NP_418470.4 zur None 43, 76
NP_418474.4 pspG None 72, 369
NP_418560.1 cutA None 43, 104
NP_418561.1 dcuA None 43, 123
NP_418569.1 yjeJ None 72, 305
NP_418579.2 poxA None 72, 279
NP_418611.1 yjfP None 72, 305
NP_418625.1 yjfZ None 67, 72
NP_418808.1 yjjK None 72, 140
YP_026192.1 yghQ None 72, 306
YP_026201.1 alx None 72, 305
YP_026212.2 nirC None 22, 43
YP_026225.1 rbbA None 43, 134
b2640 b2640 None 43, 72
b2969 yghE None 72, 279
b2973 b2973 None 72, 162
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 b2640
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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