Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_809979.1 BT_1066

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_809979.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_809979.1!

Warning: NP_809979.1 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
5800 9.50e-06 GGccTaTTg.gTg.taaTgcGa
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5801 7.60e+02 AccGGAacccc
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5922 7.40e-04 cCCATaAgGaatagC.GCCc
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5923 1.40e-02 acaCgtcCt.Cagc
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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_809979.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_809979.1

NP_809979.1 has total of 47 gene neighbors in modules 36, 99
Gene neighbors (47)
Gene Common Name Description Module membership
NP_808991.1 BT_0078 None 99, 236
NP_809977.1 BT_1064 None 36, 86
NP_809978.1 BT_1065 None 36, 319
NP_809979.1 BT_1066 None 36, 99
NP_809980.1 BT_1067 None 36, 319
NP_809981.1 BT_1068 None 36, 319
NP_810082.1 BT_1169 None 86, 99
NP_810428.1 BT_1515 None 99, 406
NP_810429.1 BT_1516 None 99, 325
NP_810704.1 BT_1791 None 99, 169
NP_810815.1 BT_1902 None 99, 406
NP_810905.1 BT_1992 None 36, 236
NP_810906.1 BT_1993 None 36, 236
NP_810939.1 BT_2026 None 99, 211
NP_811380.1 BT_2467 None 99, 121
NP_811381.1 BT_2468 None 97, 99
NP_811500.1 BT_2587 None 99, 441
NP_811559.1 BT_2646 None 36, 385
NP_811560.1 BT_2647 None 36, 385
NP_811561.1 BT_2648 None 36, 385
NP_812113.1 BT_3201 None 36, 119
NP_812114.1 BT_3202 None 36, 119
NP_812378.1 BT_3466 None 99, 356
NP_812798.1 BT_3887 None 82, 99
NP_812851.1 BT_3940 None 82, 99
NP_812879.1 BT_3968 None 99, 284
NP_812880.1 BT_3969 None 99, 406
NP_813457.1 BT_4546 None 36, 267
NP_813458.1 BT_4547 None 36, 267
NP_813459.1 BT_4548 None 36, 267
NP_813460.1 BT_4549 None 36, 267
NP_813461.1 BT_4550 None 36, 211
NP_813531.1 BT_4620 None 36, 267
NP_813532.1 BT_4621 None 36, 267
NP_813533.1 BT_4622 None 36, 267
NP_813534.1 BT_4623 None 36, 267
NP_813535.1 mpi None 36, 267
NP_813597.1 BT_4686 None 99, 134
NP_813659.1 BT_4748 None 36, 240
NP_813660.1 BT_4749 None 36, 240
NP_813669.1 BT_4758 None 99, 469
NP_813677.1 BT_4766 None 99, 325
NP_813679.1 BT_4768 None 12, 99
NP_813680.1 BT_4769 None 12, 99
NP_813681.1 BT_4770 None 12, 99
NP_813689.1 BT_4778 None 99, 345
NP_813690.1 BT_4779 None 99, 345
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_809979.1
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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