Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_811467.1 BT_2554

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_811467.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_811467.1!

Warning: NP_811467.1 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
6174 3.80e+01 gCCg.tGAatccgg
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6175 1.80e+02 C.TAccTtTGt
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6520 1.80e-01 TATcTTTG
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6521 1.40e+04 GGGGGAcGaG
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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_811467.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_811467.1

NP_811467.1 has total of 40 gene neighbors in modules 225, 404
Gene neighbors (40)
Gene Common Name Description Module membership
NP_809078.1 BT_0165 None 170, 225
NP_809079.1 BT_0166 None 136, 225
NP_809801.1 BT_0888 None 338, 404
NP_810170.1 BT_1257 None 6, 225
NP_810179.1 BT_1266 None 225, 433
NP_810229.1 BT_1316 None 338, 404
NP_810319.1 BT_1406 None 6, 225
NP_810395.1 BT_1482 None 225, 298
NP_810482.1 BT_1569 None 404, 433
NP_810578.1 BT_1665 None 170, 404
NP_810741.1 BT_1828 None 338, 404
NP_811092.1 BT_2179 None 338, 404
NP_811267.1 BT_2354 None 363, 404
NP_811268.1 BT_2355 None 225, 363
NP_811279.1 BT_2366 None 225, 314
NP_811426.1 BT_2513 None 94, 404
NP_811450.1 BT_2537 None 198, 225
NP_811466.1 BT_2553 None 56, 404
NP_811467.1 BT_2554 None 225, 404
NP_811689.1 BT_2777 None 225, 244
NP_811836.1 BT_2924 None 225, 363
NP_811838.1 BT_2926 None 6, 225
NP_812091.1 BT_3179 None 117, 225
NP_812274.1 BT_3362 None 225, 363
NP_812344.1 BT_3432 None 338, 404
NP_812402.1 BT_3490 None 6, 225
NP_812467.1 BT_3555 None 225, 338
NP_812608.1 BT_3697 None 338, 404
NP_812717.1 BT_3806 None 222, 225
NP_812718.1 BT_3807 None 222, 225
NP_812764.1 BT_3853 None 225, 363
NP_812889.1 BT_3978 None 6, 225
NP_812957.1 BT_4046 None 338, 404
NP_813356.1 BT_4445 None 338, 404
NP_813420.1 BT_4509 None 189, 404
NP_813440.1 BT_4529 None 170, 404
NP_813441.1 BT_4530 None 246, 404
NP_813494.1 BT_4583 None 338, 404
NP_813518.1 BT_4607 None 225, 363
NP_813519.1 BT_4608 None 225, 363
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_811467.1
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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