Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_811654.1 BT_2742

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_811654.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_811654.1!

Warning: NP_811654.1 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
6328 7.90e-04 atTtTtt.TAtaTTtGcacc.
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6329 3.10e+04 ACCCGC
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6418 1.30e-01 T.gTactTTTGcgccgcgatT
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6419 4.10e+03 Ta.GGAAAAatTt.tcTAa
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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_811654.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_811654.1

NP_811654.1 has total of 40 gene neighbors in modules 306, 353
Gene neighbors (40)
Gene Common Name Description Module membership
NP_809259.1 BT_0346 None 306, 353
NP_809286.1 BT_0373 None 353, 439
NP_809331.1 BT_0418 None 156, 353
NP_809536.1 BT_0623 None 170, 306
NP_809813.1 BT_0900 None 309, 353
NP_809828.1 rpmG None 231, 353
NP_810107.1 BT_1194 None 306, 336
NP_810224.1 BT_1311 None 221, 353
NP_810604.1 BT_1691 None 306, 353
NP_810760.1 BT_1847 None 306, 336
NP_810965.1 BT_2052 None 53, 353
NP_810966.1 BT_2053 None 135, 353
NP_810967.1 BT_2054 None 135, 353
NP_810968.1 BT_2055 None 135, 353
NP_810972.1 BT_2059 None 306, 353
NP_811038.1 BT_2125 None 221, 306
NP_811078.1 BT_2165 None 306, 336
NP_811141.1 BT_2228 None 177, 306
NP_811162.1 frr None 306, 314
NP_811185.1 BT_2272 None 306, 326
NP_811406.1 BT_2493 None 353, 439
NP_811652.1 tuf None 135, 353
NP_811653.1 BT_2741 None 306, 353
NP_811654.1 BT_2742 None 306, 353
NP_811665.1 BT_2753 None 306, 336
NP_811702.1 BT_2790 None 135, 353
NP_811756.1 BT_2844 None 309, 353
NP_812057.1 BT_3145 None 156, 353
NP_812270.1 BT_3358 None 135, 353
NP_812271.1 BT_3359 None 135, 353
NP_812642.1 pyrE None 170, 306
NP_812751.1 BT_3840 None 309, 353
NP_812822.1 BT_3911 None 250, 353
NP_812836.1 BT_3925 None 108, 353
NP_812892.1 BT_3981 None 273, 353
NP_813013.1 BT_4102 None 221, 306
NP_813174.1 BT_4263 None 135, 353
NP_813175.1 BT_4264 None 104, 306
NP_813279.1 BT_4368 None 309, 353
NP_813525.1 BT_4614 None 170, 306
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_811654.1
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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