Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_810424.1 BT_1511

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_810424.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_810424.1!

Warning: NP_810424.1 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
5962 1.40e-07 GCag.caaTtCcggc
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5963 5.30e-02 AcCtTtgccgtaCcgtcgT.cAc
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6138 8.60e-15 aCCgaCTgTCACTGtAcacaacCG
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6139 7.50e-14 GCAatTGtTGTCagtTaTAGTCtg
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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_810424.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_810424.1

NP_810424.1 has total of 43 gene neighbors in modules 119, 207
Gene neighbors (43)
Gene Common Name Description Module membership
NP_808931.1 BT_0018 None 119, 409
NP_808932.1 BT_0019 None 119, 409
NP_808939.1 BT_0026 None 207, 355
NP_809058.1 BT_0145 None 119, 450
NP_809059.1 BT_0146 None 119, 450
NP_809321.1 BT_0408 None 207, 336
NP_809346.1 BT_0433 None 147, 207
NP_810042.1 BT_1129 None 207, 450
NP_810043.1 BT_1130 None 97, 207
NP_810050.1 BT_1137 None 46, 119
NP_810418.1 BT_1505 None 119, 415
NP_810419.1 BT_1506 None 119, 415
NP_810424.1 BT_1511 None 119, 207
NP_810430.1 BT_1517 None 47, 207
NP_810552.1 BT_1639 None 147, 207
NP_810553.1 BT_1640 None 207, 284
NP_810617.1 BT_1704 None 207, 284
NP_810618.1 BT_1705 None 97, 207
NP_810691.1 BT_1778 None 119, 470
NP_810692.1 BT_1779 None 119, 206
NP_810693.1 BT_1780 None 119, 470
NP_810694.1 BT_1781 None 119, 470
NP_810843.1 BT_1930 None 7, 119
NP_810845.1 BT_1932 None 207, 411
NP_810893.1 BT_1980 None 207, 289
NP_810901.1 BT_1988 None 137, 207
NP_810958.1 BT_2045 None 207, 443
NP_811262.1 BT_2349 None 207, 359
NP_811445.1 BT_2532 None 119, 134
NP_811565.1 BT_2652 None 46, 207
NP_811566.1 BT_2653 None 46, 207
NP_811590.1 BT_2678 None 207, 351
NP_812094.1 BT_3182 None 207, 336
NP_812113.1 BT_3201 None 36, 119
NP_812114.1 BT_3202 None 36, 119
NP_813072.1 BT_4161 None 207, 411
NP_813341.1 BT_4430 None 119, 374
NP_813342.1 BT_4431 None 207, 456
NP_813348.1 BT_4437 None 7, 119
NP_813646.1 BT_4735 None 119, 406
NP_813662.1 BT_4751 None 46, 119
NP_813670.1 BT_4759 None 86, 119
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_810424.1
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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