Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_811930.1 BT_3018

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_811930.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_811930.1!

Warning: NP_811930.1 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
5908 2.30e+00 tGcAaAGaTAactgt
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5909 1.00e+01 TcaaGcTccATTCTTggtaTTcgA
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6168 1.10e-02 aaATtcgTaTcTTTgtctTtt
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6169 1.00e+01 GGAATTTAATTTCaTT
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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_811930.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_811930.1

NP_811930.1 has total of 39 gene neighbors in modules 92, 222
Gene neighbors (39)
Gene Common Name Description Module membership
NP_809073.1 BT_0160 None 222, 459
NP_809412.1 BT_0499 None 80, 92
NP_809416.1 BT_0503 None 92, 402
NP_809417.1 BT_0504 None 92, 402
NP_809473.1 BT_0560 None 222, 244
NP_809474.1 BT_0561 None 90, 222
NP_809475.1 BT_0562 None 222, 244
NP_809476.1 BT_0563 None 102, 222
NP_809542.1 BT_0629 None 222, 310
NP_809929.1 BT_1016 None 222, 459
NP_810332.1 BT_1419 None 92, 345
NP_810333.1 BT_1420 None 92, 345
NP_810597.1 BT_1684 None 56, 222
NP_810706.1 BT_1793 None 222, 459
NP_810710.1 BT_1797 None 92, 402
NP_810711.1 BT_1798 None 92, 413
NP_810712.1 BT_1799 None 92, 413
NP_810726.1 BT_1813 None 92, 222
NP_810727.1 BT_1814 None 92, 222
NP_810740.1 BT_1827 None 120, 222
NP_810826.1 BT_1913 None 222, 245
NP_810963.1 BT_2050 None 92, 244
NP_810981.1 BT_2068 None 92, 403
NP_811397.1 BT_2484 None 136, 222
NP_811401.1 BT_2488 None 222, 459
NP_811576.1 BT_2663 None 92, 402
NP_811577.1 BT_2664 None 92, 402
NP_811578.1 BT_2665 None 92, 402
NP_811579.1 BT_2666 None 92, 402
NP_811580.1 BT_2667 None 92, 402
NP_811581.1 BT_2668 None 92, 402
NP_811610.1 BT_2698 None 92, 402
NP_811748.1 BT_2836 None 92, 175
NP_811930.1 BT_3018 None 92, 222
NP_812305.1 BT_3393 None 222, 459
NP_812717.1 BT_3806 None 222, 225
NP_812718.1 BT_3807 None 222, 225
NP_812958.1 BT_4047 None 56, 222
NP_813397.1 BT_4486 None 222, 297
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_811930.1
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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