Organism : Escherichia coli K12 | Module List :
NP_415021.2 ybbJ

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_415021.2
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_415021.2!

Warning: NP_415021.2 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
8718 3.90e-11 acaCTcTcccTTAAccGtGcATgc
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8719 7.00e-10 cactgctGCAaCaGgAcgttttcC
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9116 5.00e+01 caTgGCgcGc.tcGgc.cGgt.CG
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9117 2.70e+03 CGaacAgCGTaCcc
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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_415021.2

Warning: No Functional annotations were found!

Module neighborhood information for NP_415021.2

NP_415021.2 has total of 48 gene neighbors in modules 131, 333
Gene neighbors (48)
Gene Common Name Description Module membership
NP_414643.1 yacG None 227, 333
NP_414673.1 panD None 113, 333
NP_414674.1 yadD None 113, 333
NP_414690.4 hrpB None 153, 333
NP_414691.1 mrcB None 260, 333
NP_414706.2 yaeI None 45, 131
NP_414731.2 rof None 105, 131
NP_414732.1 yaeQ None 105, 131
NP_414733.1 yaeJ None 105, 131
NP_414734.1 nlpE None 105, 131
NP_414742.1 gmhB None 314, 333
NP_414744.1 yafC None 110, 333
NP_414891.4 frmR None 131, 218
NP_414927.1 rdgC None 125, 333
NP_414930.3 araJ None 130, 131
NP_414937.1 malZ None 260, 333
NP_414958.4 yajL None 105, 131
NP_414959.1 panE None 105, 131
NP_414960.2 yajQ None 105, 131
NP_414975.1 ppiD None 299, 333
NP_414978.1 queC None 224, 333
NP_414999.1 ybaM None 62, 333
NP_415021.2 ybbJ None 131, 333
NP_415022.1 qmcA None 110, 131
NP_415036.1 ybbB None 105, 131
NP_415157.1 crcB None 131, 327
NP_415241.1 ybgL None 131, 198
NP_415320.1 dinG None 316, 333
NP_415361.1 deoR None 276, 333
NP_415418.1 ycaD None 10, 333
NP_415482.1 helD None 50, 333
NP_415738.2 ychO None 131, 134
NP_415850.1 fnr None 182, 333
NP_415859.1 dbpA None 175, 333
NP_415956.1 ydcR None 234, 333
NP_416113.1 ynfM None 279, 333
NP_416141.4 ydgJ None 54, 333
NP_416277.1 topB None 131, 314
NP_416278.1 selD None 131, 314
NP_416636.1 bglX None 54, 333
NP_416662.1 yeiE None 21, 131
NP_416663.1 yeiH None 21, 131
NP_416906.1 ligA None 333, 389
NP_417312.1 lplT None 333, 354
NP_417313.1 aas None 325, 333
NP_418258.1 uvrD None 22, 131
NP_418467.1 lexA None 333, 371
YP_025293.1 setA None 333, 380
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_415021.2
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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