Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_809774.1 BT_0861

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_809774.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_809774.1!

Warning: NP_809774.1 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
6246 1.30e-04 tattt.TAtaTTTGcaataaa
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6247 5.80e+04 GGGTACCG
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6448 5.40e-05 cTgattcTactC.Tt.TT.aAcgc
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6449 8.30e-03 cAtcccaTaaAtcTtCGATTGcGC
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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_809774.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_809774.1

NP_809774.1 has total of 63 gene neighbors in modules 261, 368
Gene neighbors (63)
Gene Common Name Description Module membership
NP_809180.1 BT_0267 None 168, 261
NP_809192.1 BT_0279 None 110, 261
NP_809425.1 BT_0512 None 261, 372
NP_809768.1 BT_0855 None 198, 368
NP_809769.1 BT_0856 None 152, 368
NP_809770.1 BT_0857 None 325, 368
NP_809771.1 BT_0858 None 325, 368
NP_809772.1 BT_0859 None 325, 368
NP_809773.1 BT_0860 None 368, 444
NP_809774.1 BT_0861 None 261, 368
NP_809775.1 BT_0862 None 325, 368
NP_809776.1 BT_0863 None 325, 368
NP_809777.1 BT_0864 None 325, 368
NP_809844.1 BT_0931 None 14, 261
NP_810191.1 BT_1278 None 98, 261
NP_810375.1 BT_1462 None 63, 261
NP_810782.1 BT_1869 None 95, 368
NP_810790.1 BT_1877 None 261, 282
NP_811115.1 BT_2202 None 261, 329
NP_811117.1 BT_2204 None 208, 261
NP_811130.1 BT_2217 None 308, 368
NP_811131.1 BT_2218 None 308, 368
NP_811133.1 BT_2220 None 308, 368
NP_811188.1 BT_2275 None 167, 261
NP_811240.1 BT_2327 None 158, 261
NP_811253.1 BT_2340 None 63, 261
NP_811294.1 BT_2381 None 168, 261
NP_811304.1 BT_2391 None 58, 261
NP_811376.1 BT_2463 None 261, 389
NP_811419.1 BT_2506 None 63, 261
NP_811420.1 BT_2507 None 63, 261
NP_811421.1 BT_2508 None 179, 261
NP_811422.1 BT_2509 None 179, 261
NP_811676.1 BT_2764 None 198, 261
NP_811712.1 BT_2800 None 261, 444
NP_811823.1 BT_2911 None 368, 415
NP_811824.1 BT_2912 None 198, 368
NP_811825.1 BT_2913 None 330, 368
NP_811826.1 BT_2914 None 330, 368
NP_811883.1 BT_2971 None 63, 261
NP_811968.1 BT_3056 None 261, 472
NP_812004.1 BT_3092 None 73, 368
NP_812005.1 BT_3093 None 73, 368
NP_812006.1 BT_3094 None 73, 368
NP_812007.1 BT_3095 None 73, 368
NP_812008.1 BT_3096 None 73, 368
NP_812009.1 BT_3097 None 73, 368
NP_812010.1 BT_3098 None 58, 261
NP_812066.1 BT_3154 None 261, 277
NP_812072.1 BT_3160 None 110, 261
NP_812432.1 BT_3520 None 3, 261
NP_812458.1 BT_3546 None 319, 368
NP_812531.1 BT_3620 None 91, 261
NP_812534.1 BT_3623 None 227, 261
NP_812571.1 BT_3660 None 261, 288
NP_812578.1 BT_3667 None 2, 261
NP_812659.1 BT_3748 None 208, 261
NP_812985.1 BT_4074 None 368, 399
NP_812987.1 BT_4076 None 73, 368
NP_813313.1 BT_4402 None 227, 261
NP_813396.1 BT_4485 None 117, 261
NP_813584.1 BT_4673 None 102, 261
NP_813616.1 BT_4705 None 208, 261
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_809774.1
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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