Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_809023.1 BT_0110

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_809023.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_809023.1!

Warning: NP_809023.1 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
6000 1.10e+01 CGgCcGgctc.Ttct
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6001 1.00e+01 GgCaGcaGA.g
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6474 3.00e+00 TgGaAAaaGgctgG.tGaTT
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6475 1.50e+04 ACCCATT.tT
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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_809023.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_809023.1

NP_809023.1 has total of 40 gene neighbors in modules 138, 381
Gene neighbors (40)
Gene Common Name Description Module membership
NP_809020.1 BT_0107 None 62, 381
NP_809021.1 BT_0108 None 381, 406
NP_809022.1 BT_0109 None 381, 454
NP_809023.1 BT_0110 None 138, 381
NP_809044.1 BT_0131 None 143, 381
NP_809133.1 BT_0220 None 138, 434
NP_809672.1 BT_0759 None 138, 365
NP_810373.1 BT_1460 None 138, 235
NP_810433.1 BT_1520 None 97, 138
NP_810614.1 BT_1701 None 138, 149
NP_810813.1 BT_1900 None 365, 381
NP_810871.1 BT_1958 None 190, 381
NP_810937.1 BT_2024 None 138, 443
NP_810942.1 BT_2029 None 40, 138
NP_811288.1 BT_2375 None 138, 434
NP_811502.1 BT_2589 None 138, 373
NP_811503.1 BT_2590 None 138, 453
NP_811776.1 BT_2864 None 82, 381
NP_811778.1 BT_2866 None 356, 381
NP_811779.1 BT_2867 None 82, 381
NP_811780.1 BT_2868 None 82, 381
NP_811781.1 BT_2869 None 82, 381
NP_811786.1 BT_2874 None 82, 381
NP_811790.1 BT_2878 None 82, 381
NP_811791.1 BT_2879 None 82, 381
NP_811794.1 BT_2882 None 121, 381
NP_811799.1 BT_2887 None 138, 381
NP_811800.1 BT_2888 None 138, 381
NP_812106.1 BT_3194 None 138, 472
NP_812409.1 BT_3497 None 138, 283
NP_812411.1 BT_3499 None 42, 138
NP_812595.1 BT_3684 None 138, 211
NP_812696.1 BT_3785 None 138, 434
NP_812924.1 BT_4013 None 40, 138
NP_812925.1 BT_4014 None 40, 138
NP_812941.1 BT_4030 None 23, 138
NP_813344.1 BT_4433 None 138, 406
NP_813455.1 BT_4544 None 138, 283
NP_813530.1 BT_4619 None 325, 381
NP_813671.1 BT_4760 None 119, 138
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_809023.1
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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