Organism : Escherichia coli K12 | Module List :
NP_415234.1 ybfD

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_415234.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_415234.1!

Warning: NP_415234.1 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
8526 4.80e-11 ATGttTAAAAATTGAGATATTCc
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8527 2.00e-09 AAatacTCcTTAcatAatTAAGGA
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8898 2.40e-03 TTGcAcTaAaTaaTtCgcaTTtTa
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8899 5.80e-06 aaAtaTtGAgatAttcctaATTac
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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_415234.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_415234.1

NP_415234.1 has total of 43 gene neighbors in modules 34, 222
Gene neighbors (43)
Gene Common Name Description Module membership
NP_415234.1 ybfD None 34, 222
NP_415513.2 torS None 222, 316
NP_415828.1 ycjP None 15, 34
NP_415926.4 ynbA None 53, 222
NP_415970.4 ansP None 222, 249
NP_415977.1 ydcC None 34, 317
NP_415993.1 fdnI None 222, 290
NP_416461.1 rcsA None 222, 301
NP_416508.1 yeeU None 20, 34
NP_416550.1 wzxC None 34, 369
NP_416775.1 yfbM None 45, 222
NP_416801.2 yfcC None 153, 222
NP_416980.1 hyfE None 34, 208
NP_416982.1 hyfG None 208, 222
NP_417392.1 scpA None 193, 222
NP_417393.1 argK None 193, 222
NP_417394.4 scpB None 222, 244
NP_417557.1 ygjQ None 34, 326
NP_417861.1 yhgE None 222, 330
NP_417941.1 yhhI None 34, 222
NP_418003.1 yhjX None 34, 205
NP_418044.1 yiaW None 34, 404
NP_418111.1 yicE None 38, 222
NP_418272.1 metR None 222, 303
NP_418342.1 rhaR None 179, 222
NP_418343.1 rhaT None 222, 396
NP_418441.1 arpA None 34, 404
NP_418504.1 mdtP None 34, 326
NP_418505.2 mdtO None 34, 326
NP_418506.1 mdtN None 34, 326
NP_418508.1 alsK None 34, 166
NP_418554.1 yjdL None 134, 222
NP_418555.1 cadA None 222, 410
NP_418556.1 cadB None 222, 396
NP_418564.2 fxsA None 213, 222
NP_418614.4 ulaA None 34, 166
NP_418776.1 yjjL None 222, 303
NP_418784.4 yjjP None 216, 222
NP_418817.1 creD None 92, 222
YP_026182.1 ascF None 34, 102
b0257 b0257 None 200, 222
b0705 ybfL None 34, 222
b4205 ytfA None 34, 191
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_415234.1
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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