Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_812689.1 BT_3778

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_812689.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_812689.1!

Warning: NP_812689.1 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
6286 2.50e+01 a.CCaat.gAg.tAgagtggTtgG
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6287 8.10e+03 TaTccTCCtcCTcatgagtggcTg
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6422 7.70e+00 ataTataAAaaAgAA
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6423 2.30e+04 GaGGCGC
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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_812689.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_812689.1

NP_812689.1 has total of 49 gene neighbors in modules 282, 355
Gene neighbors (49)
Gene Common Name Description Module membership
NP_808939.1 BT_0026 None 207, 355
NP_809166.1 BT_0253 None 88, 355
NP_809356.1 BT_0443 None 178, 282
NP_809357.1 BT_0444 None 178, 282
NP_809704.1 BT_0791 None 3, 355
NP_809705.1 BT_0792 None 3, 355
NP_809706.1 BT_0793 None 3, 355
NP_809707.1 xylE None 3, 355
NP_809892.1 BT_0979 None 2, 355
NP_809893.1 BT_0980 None 2, 355
NP_809894.1 BT_0981 None 355, 449
NP_810160.1 BT_1247 None 262, 355
NP_810231.1 BT_1318 None 355, 400
NP_810232.1 BT_1319 None 355, 429
NP_810669.1 BT_1756 None 42, 282
NP_810789.1 BT_1876 None 88, 282
NP_810790.1 BT_1877 None 261, 282
NP_810816.1 BT_1903 None 282, 411
NP_811017.1 BT_2104 None 278, 282
NP_811018.1 BT_2105 None 278, 282
NP_811019.1 BT_2106 None 45, 282
NP_811281.1 BT_2368 None 355, 446
NP_811297.1 BT_2384 None 299, 355
NP_811370.1 BT_2457 None 47, 282
NP_811371.1 BT_2458 None 47, 282
NP_811372.1 BT_2459 None 47, 282
NP_811374.1 BT_2461 None 47, 282
NP_811375.1 BT_2462 None 47, 282
NP_811377.1 BT_2464 None 45, 282
NP_811474.1 BT_2561 None 209, 282
NP_811592.1 BT_2680 None 50, 282
NP_811827.1 BT_2915 None 282, 330
NP_811833.1 BT_2921 None 116, 282
NP_812119.1 BT_3207 None 282, 411
NP_812120.1 BT_3208 None 282, 429
NP_812204.1 BT_3292 None 278, 282
NP_812310.1 BT_3398 None 114, 282
NP_812420.1 BT_3508 None 3, 355
NP_812430.1 BT_3518 None 282, 355
NP_812589.1 BT_3678 None 282, 354
NP_812686.1 BT_3775 None 355, 390
NP_812687.1 BT_3776 None 282, 390
NP_812688.1 BT_3777 None 355, 390
NP_812689.1 BT_3778 None 282, 355
NP_812690.1 BT_3779 None 282, 355
NP_813252.1 BT_4341 None 6, 355
NP_813491.1 BT_4580 None 355, 411
NP_813495.1 gcvT None 355, 449
NP_813617.1 BT_4706 None 49, 282
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_812689.1
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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