Organism : Escherichia coli K12 | Module List :
NP_417045.4 yphH

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_417045.4
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_417045.4!

Warning: NP_417045.4 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
8850 4.00e+03 TC.GgCAG
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8851 8.40e+03 CgcttTgcgtctt.tcg.GtC
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9100 2.00e+02 AAaAa.cCgGA
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9101 1.20e+03 tgctGGaGaGa
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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_417045.4

Warning: No Functional annotations were found!

Module neighborhood information for NP_417045.4

NP_417045.4 has total of 49 gene neighbors in modules 198, 325
Gene neighbors (49)
Gene Common Name Description Module membership
NP_414547.1 yaaA None 91, 325
NP_414670.1 yadH None 198, 338
NP_414675.1 panC None 198, 419
NP_414980.2 cof None 198, 316
NP_415240.1 ybgK None 198, 419
NP_415241.1 ybgL None 131, 198
NP_415242.1 nei None 198, 241
NP_415399.4 macA None 114, 325
NP_415410.1 ftsK None 198, 409
NP_415698.1 ycgM None 198, 257
NP_416240.1 yniB None 41, 198
NP_416272.2 ynjF None 198, 354
NP_416355.1 yobA None 198, 227
NP_416364.1 eda None 198, 284
NP_416422.1 pgsA None 198, 372
NP_416467.1 yedI None 217, 325
NP_416469.1 vsr None 163, 198
NP_416495.1 cobT None 171, 198
NP_416496.1 cobS None 171, 198
NP_416497.1 cobU None 198, 243
NP_416860.4 yfdP None 101, 198
NP_416861.1 yfdQ None 101, 198
NP_416929.4 ypeA None 104, 198
NP_416945.2 yffS None 91, 325
NP_417045.4 yphH None 198, 325
NP_417196.1 ascB None 25, 325
NP_417313.1 aas None 325, 333
NP_417314.1 galR None 198, 200
NP_417572.2 yqjF None 67, 325
NP_417617.1 yraN None 198, 321
NP_417621.2 yraR None 225, 325
NP_417630.1 mtr None 282, 325
NP_417711.1 tldD None 155, 198
NP_417815.1 yhfA None 198, 229
NP_417931.4 yhhT None 258, 325
NP_417981.1 yhjG None 211, 325
NP_418144.2 yidR None 219, 325
NP_418326.2 yiiF None 325, 410
NP_418334.1 frvX None 279, 325
NP_418485.1 yjcC None 217, 325
NP_418541.1 adiA None 236, 325
NP_418545.1 yjdF None 162, 325
NP_418673.4 yjgK None 198, 418
NP_418698.1 insG None 171, 325
NP_418760.1 yjiR None 282, 325
NP_418771.1 mrr None 198, 243
NP_418802.1 yjjJ None 279, 325
YP_025310.1 yedK None 211, 325
b4343 b4343 None 282, 325
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_417045.4
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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