Organism : Escherichia coli K12 | Module List :
NP_418101.1 yicC

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_418101.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_418101.1!

Warning: NP_418101.1 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
8736 1.20e+00 Gcc.cG.aTTaTaCGGacTTctGg
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8737 6.70e+02 GGCgTGAA
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9020 1.60e-01 CgccGCgCgccgCaaaAgcGg
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9021 6.70e+01 gCttcGgctTGCtG
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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_418101.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_418101.1

NP_418101.1 has total of 52 gene neighbors in modules 140, 284
Gene neighbors (52)
Gene Common Name Description Module membership
NP_414714.1 frr None 140, 263
NP_414750.1 rnhA None 284, 314
NP_415318.1 rhlE None 140, 379
NP_415347.1 moeB None 259, 284
NP_415356.1 yliG None 140, 144
NP_415710.1 ldcA None 284, 302
NP_415752.1 galU None 157, 284
NP_415769.1 yciA None 54, 140
NP_415785.1 rluB None 140, 379
NP_415790.1 topA None 140, 178
NP_415798.2 yciH None 140, 411
NP_415860.1 ttcA None 140, 218
NP_415932.1 ydcF None 284, 292
NP_416037.2 yneE None 232, 284
NP_416169.1 rnt None 140, 277
NP_416174.1 ydhP None 284, 354
NP_416224.1 btuD None 284, 376
NP_416263.1 xthA None 265, 284
NP_416364.1 eda None 198, 284
NP_416421.1 yecA None 27, 284
NP_416676.4 yeiP None 140, 367
NP_416988.1 yfgO None 228, 284
NP_417076.1 yfiF None 106, 140
NP_417284.1 fucU None 284, 298
NP_417412.1 speB None 140, 253
NP_417419.1 yggI None 140, 143
NP_417437.1 yggX None 284, 314
NP_417514.4 yqiC None 113, 284
NP_417528.1 cca None 37, 284
NP_417531.1 ygiH None 284, 316
NP_417615.1 yraL None 54, 284
NP_417634.1 rpsO None 138, 140
NP_417642.1 secG None 140, 277
NP_417648.4 greA None 140, 263
NP_417650.1 obgE None 140, 263
NP_417651.1 yhbE None 140, 263
NP_417932.1 acpT None 284, 301
NP_417949.1 yhiN None 72, 140
NP_418068.1 yibN None 229, 284
NP_418069.1 gpmM None 229, 284
NP_418101.1 yicC None 140, 284
NP_418213.1 yifE None 143, 284
NP_418223.1 ppiC None 84, 140
NP_418371.1 rpmE None 140, 218
NP_418425.1 hemE None 27, 284
NP_418426.2 nfi None 27, 284
NP_418466.1 dgkA None 243, 284
NP_418801.1 deoD None 71, 284
NP_418808.1 yjjK None 72, 140
NP_418820.1 yjtD None 282, 284
YP_001491547.1 rph None 140, 277
YP_026280.1 nudC None 265, 284
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_418101.1
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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