Organism : Escherichia coli K12 | Module List :
b3777 yifN

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for b3777
(Mouseover regulator name to see its description)

Warning: No Regulators were found for b3777!

Warning: b3777 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
8540 2.60e+01 GaAGaaAAcag
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8541 3.00e+01 T.aTTTTTCgtaATG
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8742 1.50e+00 ACcttttGttaTaaCTtgcTCcG
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8743 1.10e+01 CcCttTtGaCaAGgGCgAcag
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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 b3777

Warning: No Functional annotations were found!

Module neighborhood information for b3777

b3777 has total of 48 gene neighbors in modules 42, 143
Gene neighbors (48)
Gene Common Name Description Module membership
NP_414665.1 cueO None 42, 62
NP_414700.1 btuF None 42, 175
NP_414717.2 cdsA None 42, 188
NP_414976.1 ybaV None 42, 48
NP_414992.1 maa None 42, 73
NP_414994.1 ybaJ None 42, 249
NP_415112.1 ybdJ None 42, 255
NP_415724.2 ychM None 42, 354
NP_415848.1 ynaJ None 42, 255
NP_415953.1 yncJ None 42, 101
NP_416052.1 ydeH None 42, 340
NP_416089.1 ydfA None 42, 249
NP_416339.1 yebO None 42, 327
NP_416340.1 mgrB None 42, 79
NP_416347.1 yebS None 42, 114
NP_416357.1 yobB None 42, 210
NP_416628.1 yehS None 42, 344
NP_416896.4 yfeA None 42, 76
NP_417000.1 yfgH None 42, 216
NP_417001.1 yfgI None 42, 167
NP_417005.2 yfgJ None 42, 114
NP_417272.1 yqcC None 143, 218
NP_417274.1 queF None 143, 393
NP_417318.1 araE None 42, 298
NP_417419.1 yggI None 140, 143
NP_417503.1 yqiA None 143, 251
NP_417724.4 panF None 42, 76
NP_417892.1 yhgN None 42, 43
NP_418030.1 ysaA None 143, 289
NP_418213.1 yifE None 143, 284
NP_418251.1 cyaY None 120, 143
NP_418278.1 yigP None 68, 143
NP_418279.1 ubiB None 68, 143
NP_418280.4 tatA None 143, 180
NP_418282.1 tatC None 52, 143
NP_418292.1 hemG None 143, 219
NP_418355.1 yiiQ None 143, 395
NP_418356.1 yiiR None 143, 228
NP_418639.1 ytfL None 42, 185
NP_418641.1 ytfM None 143, 219
NP_418642.1 ytfN None 74, 143
NP_418643.1 ytfP None 13, 143
YP_026256.2 rffC None 143, 228
YP_026269.1 ubiE None 68, 143
YP_026270.1 tatB None 13, 143
b3776 b3776 None 143, 302
b3777 yifN None 42, 143
b4223 b4223 None 84, 143
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 b3777
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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