Organism : Escherichia coli K12 | Module List :
NP_416721.1 rcsB

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_416721.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_416721.1!

Warning: NP_416721.1 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
8760 1.20e+03 AggcAaaCATCtAaaAGGaaAg
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8761 1.50e+03 TTGCGcTGtcattGc
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8934 1.10e+03 gGCgtTtcctCgcCgatTtCcCtC
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8935 2.10e+03 CCagCc.GGcG
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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_416721.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_416721.1

NP_416721.1 has total of 45 gene neighbors in modules 152, 241
Gene neighbors (45)
Gene Common Name Description Module membership
NP_414549.1 talB None 123, 152
NP_414572.1 dapB None 152, 323
NP_414667.4 hpt None 152, 218
NP_414736.1 proS None 152, 379
NP_414772.1 pepD None 113, 152
NP_414821.1 yagU None 86, 241
NP_414903.4 hemB None 54, 152
NP_414949.1 ribE None 152, 213
NP_414970.1 tig None 152, 277
NP_415058.1 ppiB None 152, 299
NP_415139.2 ahpF None 49, 152
NP_415242.1 nei None 198, 241
NP_415271.1 nadA None 241, 302
NP_415272.1 pnuC None 241, 268
NP_415335.1 ompX None 152, 157
NP_415371.1 ybjC None 152, 382
NP_415372.1 nfsA None 152, 382
NP_415373.1 rimK None 152, 408
NP_415408.1 trxB None 35, 152
NP_415413.1 serS None 123, 241
NP_415438.1 kdsB None 152, 393
NP_415450.1 asnS None 152, 178
NP_415788.1 sohB None 123, 152
NP_415804.1 fabI None 152, 260
NP_415930.1 azoR None 152, 224
NP_416344.1 prc None 168, 241
NP_416346.3 yebR None 227, 241
NP_416523.1 hisG None 241, 323
NP_416524.1 hisD None 241, 323
NP_416525.1 hisC None 241, 323
NP_416526.4 hisB None 241, 323
NP_416527.1 hisH None 241, 323
NP_416528.2 hisA None 241, 323
NP_416529.1 hisF None 241, 323
NP_416530.1 hisI None 241, 323
NP_416533.1 gnd None 56, 241
NP_416720.1 rcsD None 241, 378
NP_416721.1 rcsB None 152, 241
NP_416770.1 elaA None 62, 152
NP_416771.4 rbn None 152, 343
NP_416915.1 yfeS None 52, 241
NP_417177.1 alaS None 241, 246
NP_417897.1 yhhX None 210, 241
NP_418152.1 yidA None 241, 358
NP_418571.1 efp None 125, 152
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_416721.1
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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