Organism : Escherichia coli K12 | Module List :
NP_415026.1 ybbO

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_415026.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_415026.1!

Warning: NP_415026.1 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
8668 2.70e+03 AtCATTtTCaT
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8669 1.90e+03 atcGCcAGccA
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9078 7.40e-01 GCacggTtggctaac
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9079 6.30e+00 CagCgcCggcA.ggTgtAAAc
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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 NP_415026.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_415026.1

NP_415026.1 has total of 46 gene neighbors in modules 106, 314
Gene neighbors (46)
Gene Common Name Description Module membership
NP_414669.1 yadG None 157, 314
NP_414699.1 yadS None 106, 128
NP_414710.1 map None 314, 324
NP_414742.1 gmhB None 314, 333
NP_414750.1 rnhA None 284, 314
NP_414921.2 yaiI None 106, 314
NP_414931.1 sbcC None 106, 314
NP_414967.1 ampG None 106, 128
NP_415000.1 priC None 62, 106
NP_415026.1 ybbO None 106, 314
NP_415027.1 tesA None 1, 314
NP_415057.1 lpxH None 299, 314
NP_415144.1 rna None 223, 314
NP_415210.1 fldA None 113, 314
NP_415267.1 tolA None 26, 314
NP_415380.1 rumB None 78, 106
NP_415411.2 lolA None 209, 314
NP_415442.1 mukF None 106, 121
NP_415443.1 mukE None 106, 121
NP_415610.1 fabD None 239, 314
NP_415786.1 btuR None 106, 188
NP_415935.2 cybB None 218, 314
NP_415964.1 ydcZ None 106, 213
NP_416168.1 gloA None 314, 417
NP_416277.1 topB None 131, 314
NP_416278.1 selD None 131, 314
NP_416279.1 ydjA None 299, 314
NP_416374.1 ruvB None 106, 366
NP_416638.4 pbpG None 123, 314
NP_416697.1 narP None 106, 377
NP_416806.1 folX None 224, 314
NP_417049.1 yfhA None 8, 314
NP_417076.1 yfiF None 106, 140
NP_417179.1 recA None 106, 157
NP_417434.4 yggL None 138, 314
NP_417436.1 mutY None 138, 314
NP_417437.1 yggX None 284, 314
NP_417500.1 mdaB None 113, 314
NP_417753.1 rplQ None 106, 138
NP_417770.1 rpsQ None 106, 336
NP_417881.1 glpR None 106, 393
NP_417927.1 sirA None 106, 380
NP_418365.1 menA None 100, 106
NP_418409.1 nusG None 106, 277
NP_418415.1 rpoC None 106, 253
YP_026220.1 glpG None 314, 393
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 NP_415026.1
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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