Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_810898.1 BT_1985

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_810898.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_810898.1!

Warning: NP_810898.1 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
5852 8.00e+04 GTAacAGaCaG
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5853 1.50e+05 CCAACC
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5950 1.70e-13 TttcTAtaTTTGca
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5951 1.50e+02 ctaCAAAgaTAaa
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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_810898.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_810898.1

NP_810898.1 has total of 53 gene neighbors in modules 63, 113
Gene neighbors (53)
Gene Common Name Description Module membership
NP_809089.1 BT_0176 None 113, 440
NP_809194.1 BT_0281 None 113, 273
NP_809324.1 BT_0411 None 100, 113
NP_809472.1 BT_0559 None 102, 113
NP_809609.1 BT_0696 None 113, 126
NP_810005.1 BT_1092 None 63, 136
NP_810006.1 BT_1093 None 63, 136
NP_810148.1 BT_1235 None 113, 440
NP_810152.1 BT_1239 None 100, 113
NP_810168.1 BT_1255 None 113, 221
NP_810169.1 BT_1256 None 113, 221
NP_810215.1 BT_1302 None 63, 152
NP_810216.1 BT_1303 None 63, 152
NP_810217.1 BT_1304 None 63, 152
NP_810218.1 BT_1305 None 63, 152
NP_810219.1 BT_1306 None 63, 152
NP_810375.1 BT_1462 None 63, 261
NP_810658.1 BT_1745 None 113, 126
NP_810736.1 BT_1823 None 63, 227
NP_810737.1 BT_1824 None 63, 227
NP_810738.1 BT_1825 None 63, 208
NP_810739.1 BT_1826 None 63, 320
NP_810810.1 BT_1897 None 63, 189
NP_810835.1 BT_1922 None 113, 124
NP_810897.1 BT_1984 None 63, 113
NP_810898.1 BT_1985 None 63, 113
NP_810925.1 BT_2012 None 113, 438
NP_811083.1 BT_2170 None 63, 150
NP_811084.1 BT_2171 None 63, 150
NP_811100.1 BT_2187 None 113, 428
NP_811183.1 BT_2270 None 100, 113
NP_811187.1 BT_2274 None 100, 113
NP_811253.1 BT_2340 None 63, 261
NP_811299.1 BT_2386 None 63, 87
NP_811419.1 BT_2506 None 63, 261
NP_811420.1 BT_2507 None 63, 261
NP_811609.1 BT_2697 None 63, 65
NP_811644.1 BT_2732 None 63, 438
NP_811684.1 BT_2772 None 63, 73
NP_811685.1 BT_2773 None 63, 73
NP_811883.1 BT_2971 None 63, 261
NP_812108.1 BT_3196 None 107, 113
NP_812326.1 BT_3414 None 113, 440
NP_812460.1 BT_3548 None 63, 152
NP_812554.1 BT_3643 None 68, 113
NP_812649.1 BT_3738 None 63, 152
NP_812716.1 BT_3805 None 113, 124
NP_812791.1 BT_3880 None 23, 63
NP_813110.1 BT_4199 None 63, 415
NP_813423.1 BT_4512 None 113, 124
NP_813426.1 BT_4515 None 63, 428
NP_813607.1 BT_4696 None 113, 244
NP_813627.1 BT_4716 None 109, 113
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_810898.1
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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