Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_813654.1 BT_4743

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_813654.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_813654.1!

Warning: NP_813654.1 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
5820 2.10e-20 GacaTcTGc.GaCAttTcctGaca
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5821 7.60e+02 GttG.aAgaCg
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6524 2.70e+03 agtgcATacgttaAgtattCCgcC
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6525 2.10e+04 CCTTTcGG
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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_813654.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_813654.1

NP_813654.1 has total of 50 gene neighbors in modules 46, 406
Gene neighbors (50)
Gene Common Name Description Module membership
NP_808917.1 BT_0004 None 365, 406
NP_808919.1 BT_0006 None 406, 427
NP_808990.1 BT_0077 None 46, 443
NP_809021.1 BT_0108 None 381, 406
NP_809695.1 BT_0782 None 252, 406
NP_809764.1 BT_0851 None 121, 406
NP_810050.1 BT_1137 None 46, 119
NP_810081.1 BT_1168 None 373, 406
NP_810087.1 BT_1174 None 151, 406
NP_810428.1 BT_1515 None 99, 406
NP_810478.1 BT_1565 None 16, 406
NP_810698.1 BT_1785 None 46, 283
NP_810699.1 BT_1786 None 46, 283
NP_810803.1 BT_1890 None 46, 263
NP_810814.1 BT_1901 None 283, 406
NP_810815.1 BT_1902 None 99, 406
NP_810833.1 BT_1920 None 211, 406
NP_810903.1 BT_1990 None 46, 454
NP_811336.1 BT_2423 None 42, 46
NP_811337.1 BT_2424 None 42, 46
NP_811338.1 BT_2425 None 42, 46
NP_811356.1 BT_2443 None 15, 406
NP_811378.1 BT_2465 None 45, 406
NP_811379.1 BT_2466 None 45, 406
NP_811382.1 BT_2469 None 46, 97
NP_811403.1 BT_2490 None 252, 406
NP_811489.1 BT_2576 None 149, 406
NP_811516.1 BT_2603 None 46, 240
NP_811517.1 BT_2604 None 46, 240
NP_811524.1 BT_2611 None 46, 453
NP_811525.1 BT_2612 None 46, 453
NP_811527.1 BT_2614 None 46, 453
NP_811557.1 BT_2644 None 46, 409
NP_811565.1 BT_2652 None 46, 207
NP_811566.1 BT_2653 None 46, 207
NP_811596.1 BT_2684 None 145, 406
NP_811768.1 BT_2856 None 315, 406
NP_811769.1 BT_2857 None 315, 406
NP_811770.1 BT_2858 None 315, 406
NP_811898.1 BT_2986 None 169, 406
NP_811934.1 BT_3022 None 145, 406
NP_812826.1 BT_3915 None 46, 252
NP_812880.1 BT_3969 None 99, 406
NP_813134.1 BT_4223 None 46, 365
NP_813251.1 BT_4340 None 319, 406
NP_813344.1 BT_4433 None 138, 406
NP_813646.1 BT_4735 None 119, 406
NP_813654.1 BT_4743 None 46, 406
NP_813662.1 BT_4751 None 46, 119
NP_813663.1 BT_4752 None 46, 409
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_813654.1
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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