Organism : Escherichia coli K12 | Module List :
NP_416327.1 nudL

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_416327.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_416327.1!

Warning: NP_416327.1 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
9132 7.00e-01 cGCGC.ctgAACTccgGcA
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9133 3.50e+03 tCGc.aATTtTccc
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9152 2.60e+00 TcCTG.CtctactctctaTGt
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9153 7.30e+02 GCgcTaattaTTTCA
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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_416327.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_416327.1

NP_416327.1 has total of 48 gene neighbors in modules 341, 351
Gene neighbors (48)
Gene Common Name Description Module membership
NP_414590.1 folA None 101, 341
NP_414655.1 pdhR None 35, 351
NP_414715.1 dxr None 263, 351
NP_414913.1 yaiY None 341, 360
NP_415014.1 ybaK None 133, 351
NP_415290.1 ybhH None 290, 341
NP_415346.4 fsaA None 270, 341
NP_415470.1 pqiA None 76, 341
NP_415472.2 ymbA None 78, 341
NP_415479.1 sxy None 75, 341
NP_415511.1 ymcE None 257, 341
NP_415581.1 yceB None 257, 351
NP_415627.1 ndh None 35, 351
NP_415630.1 bhsA None 255, 351
NP_415663.1 ymfK None 45, 351
NP_415805.1 ycjD None 101, 341
NP_415856.1 ydaL None 327, 341
NP_415963.1 ydcY None 351, 406
NP_416153.1 pdxY None 171, 351
NP_416154.1 tyrS None 218, 351
NP_416325.1 yoaH None 351, 380
NP_416326.1 pabB None 341, 351
NP_416327.1 nudL None 341, 351
NP_416348.2 yebT None 223, 341
NP_416362.1 yebG None 341, 366
NP_416424.1 uvrY None 210, 351
NP_416425.1 yecF None 59, 351
NP_416546.1 galF None 277, 351
NP_416571.1 yegE None 211, 341
NP_416645.1 dusC None 91, 341
NP_416646.1 yohJ None 341, 398
NP_416647.1 yohK None 135, 341
NP_416763.1 menE None 37, 341
NP_416764.1 menC None 37, 341
NP_416899.1 gltX None 351, 397
NP_417054.2 tadA None 341, 366
NP_417323.2 yqeH None 87, 341
NP_417487.1 yqhH None 341, 354
NP_417705.2 yhcN None 41, 351
NP_417929.4 dcrB None 157, 351
NP_418155.1 recF None 142, 351
NP_418198.1 mioC None 227, 351
NP_418503.1 fdhF None 316, 341
NP_418572.4 sugE None 41, 341
NP_418676.1 rraB None 27, 351
NP_418774.2 yjiY None 341, 373
b4274 b4274 None 341, 359
b4404 b4404 None 59, 351
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_416327.1
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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