Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_810453.1 BT_1540

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_810453.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_810453.1!

Warning: NP_810453.1 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
5998 1.10e-04 cggcGgAaaccTgCg.a.gaATA
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5999 4.90e+02 GccGtGcAgct
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6356 9.60e+02 ttttt.caaAtATAc
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6357 8.00e+03 AaTaaAAACAg
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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_810453.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_810453.1

NP_810453.1 has total of 48 gene neighbors in modules 137, 321
Gene neighbors (48)
Gene Common Name Description Module membership
NP_809048.1 BT_0135 None 56, 321
NP_809066.1 BT_0153 None 137, 324
NP_809339.1 BT_0426 None 137, 324
NP_809455.1 BT_0542 None 289, 321
NP_809582.1 BT_0669 None 137, 262
NP_809697.1 BT_0784 None 137, 324
NP_809708.1 BT_0795 None 137, 262
NP_809794.1 BT_0881 None 262, 321
NP_809834.1 BT_0921 None 137, 316
NP_809871.1 BT_0958 None 37, 321
NP_809884.1 BT_0971 None 321, 369
NP_810091.1 BT_1178 None 321, 359
NP_810327.1 BT_1414 None 137, 324
NP_810328.1 BT_1415 None 137, 324
NP_810329.1 BT_1416 None 137, 324
NP_810330.1 nrfA None 137, 324
NP_810331.1 BT_1418 None 137, 324
NP_810337.1 BT_1424 None 137, 272
NP_810360.1 BT_1447 None 27, 321
NP_810453.1 BT_1540 None 137, 321
NP_810454.1 BT_1541 None 137, 324
NP_810603.1 BT_1690 None 137, 324
NP_810744.1 BT_1831 None 289, 321
NP_810797.1 BT_1884 None 137, 324
NP_810798.1 BT_1885 None 137, 324
NP_810799.1 BT_1886 None 137, 324
NP_810800.1 BT_1887 None 137, 324
NP_810806.1 BT_1893 None 137, 324
NP_810823.1 BT_1910 None 137, 324
NP_810901.1 BT_1988 None 137, 207
NP_810902.1 BT_1989 None 137, 262
NP_810982.1 BT_2069 None 137, 358
NP_811029.1 BT_2116 None 137, 324
NP_811087.1 BT_2174 None 37, 321
NP_811251.1 BT_2338 None 137, 324
NP_811385.1 BT_2472 None 137, 324
NP_811440.1 BT_2527 None 37, 321
NP_811567.1 BT_2654 None 137, 320
NP_811666.1 BT_2754 None 37, 321
NP_811951.1 BT_3039 None 137, 415
NP_812469.1 BT_3557 None 6, 137
NP_812584.1 BT_3673 None 285, 321
NP_813132.1 BT_4221 None 37, 321
NP_813142.1 BT_4231 None 137, 324
NP_813253.1 BT_4342 None 37, 321
NP_813343.1 BT_4432 None 137, 358
NP_813370.1 BT_4459 None 117, 321
NP_813385.1 BT_4474 None 56, 137
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_810453.1
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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