Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_811813.1 BT_2901

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_811813.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_811813.1!

Warning: NP_811813.1 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
6052 3.60e+03 cgAcA.ggg.taGcAgtgG
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6053 1.00e+04 CCCGGA
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6134 1.00e+03 GgGcgGcA
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6135 1.80e+03 ccACtc.cA.GaCA
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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_811813.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_811813.1

NP_811813.1 has total of 44 gene neighbors in modules 164, 205
Gene neighbors (44)
Gene Common Name Description Module membership
NP_809185.1 BT_0272 None 110, 164
NP_810382.1 BT_1469 None 29, 164
NP_810383.1 BT_1470 None 164, 192
NP_810690.1 BT_1777 None 141, 205
NP_811116.1 BT_2203 None 29, 164
NP_811763.1 BT_2851 None 205, 401
NP_811764.1 BT_2852 None 141, 205
NP_811765.1 BT_2853 None 205, 319
NP_811766.1 BT_2854 None 110, 205
NP_811813.1 BT_2901 None 164, 205
NP_811814.1 BT_2902 None 164, 205
NP_811815.1 BT_2903 None 205, 401
NP_811816.1 BT_2904 None 164, 205
NP_811817.1 BT_2905 None 205, 401
NP_811818.1 BT_2906 None 205, 401
NP_811819.1 BT_2907 None 164, 205
NP_811820.1 BT_2908 None 164, 205
NP_811821.1 BT_2909 None 164, 205
NP_811822.1 BT_2910 None 205, 322
NP_811932.1 BT_3020 None 164, 192
NP_811977.1 BT_3065 None 205, 401
NP_811999.1 BT_3087 None 164, 192
NP_812000.1 BT_3088 None 164, 192
NP_812002.1 BT_3090 None 110, 164
NP_812042.1 BT_3130 None 164, 210
NP_812044.1 BT_3132 None 164, 456
NP_812045.1 BT_3133 None 164, 456
NP_812069.1 BT_3157 None 205, 354
NP_812070.1 BT_3158 None 29, 205
NP_812071.1 BT_3159 None 29, 205
NP_812084.1 BT_3172 None 141, 164
NP_812864.1 BT_3953 None 164, 192
NP_812865.1 BT_3954 None 164, 192
NP_812866.1 BT_3955 None 164, 192
NP_812991.1 BT_4080 None 205, 401
NP_812992.1 BT_4081 None 205, 401
NP_812993.1 BT_4082 None 205, 401
NP_812994.1 BT_4083 None 205, 401
NP_812995.1 BT_4084 None 205, 401
NP_813635.1 BT_4724 None 29, 164
NP_813636.1 BT_4725 None 29, 164
NP_813637.1 BT_4726 None 29, 164
NP_813638.1 BT_4727 None 29, 164
NP_813639.1 BT_4728 None 29, 164
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_811813.1
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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