Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_810819.1 BT_1906

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_810819.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_810819.1!

Warning: NP_810819.1 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
6428 1.30e-07 tcTAtCTTTGCagc
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6429 1.40e+02 CACAGCCATACTGGTACGGAGTGG
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6542 1.50e-03 c.cTAtAtTTGCAgC
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6543 4.00e+04 CTGTCCGC
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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_810819.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_810819.1

NP_810819.1 has total of 67 gene neighbors in modules 358, 415
Gene neighbors (67)
Gene Common Name Description Module membership
NP_809084.1 BT_0171 None 163, 415
NP_809111.1 BT_0198 None 179, 358
NP_809271.1 BT_0358 None 179, 358
NP_809464.1 asnB None 415, 472
NP_809552.1 BT_0639 None 163, 358
NP_809660.1 BT_0747 None 358, 364
NP_809866.1 BT_0953 None 16, 415
NP_809895.1 BT_0982 None 235, 415
NP_810145.1 BT_1232 None 347, 358
NP_810161.1 BT_1248 None 277, 358
NP_810418.1 BT_1505 None 119, 415
NP_810419.1 BT_1506 None 119, 415
NP_810425.1 BT_1512 None 42, 415
NP_810456.1 BT_1543 None 179, 358
NP_810778.1 BT_1865 None 9, 415
NP_810818.1 BT_1905 None 58, 415
NP_810819.1 BT_1906 None 358, 415
NP_810877.1 BT_1964 None 358, 374
NP_810878.1 BT_1965 None 358, 374
NP_810880.1 BT_1967 None 358, 374
NP_810982.1 BT_2069 None 137, 358
NP_811009.1 BT_2096 None 349, 358
NP_811010.1 BT_2097 None 349, 358
NP_811015.1 BT_2102 None 273, 358
NP_811178.1 BT_2265 None 399, 415
NP_811256.1 BT_2343 None 356, 358
NP_811259.1 BT_2346 None 144, 358
NP_811269.1 BT_2356 None 179, 358
NP_811270.1 BT_2357 None 179, 358
NP_811272.1 BT_2359 None 9, 415
NP_811292.1 BT_2379 None 347, 358
NP_811345.1 BT_2432 None 50, 415
NP_811442.1 BT_2529 None 67, 415
NP_811449.1 BT_2536 None 242, 358
NP_811468.1 BT_2555 None 358, 472
NP_811488.1 BT_2575 None 149, 358
NP_811692.1 BT_2780 None 9, 415
NP_811772.1 BT_2860 None 347, 358
NP_811823.1 BT_2911 None 368, 415
NP_811840.1 BT_2928 None 235, 358
NP_811842.1 BT_2930 None 134, 415
NP_811877.1 BT_2965 None 415, 429
NP_811894.1 BT_2982 None 319, 358
NP_811911.1 BT_2999 None 415, 416
NP_811951.1 BT_3039 None 137, 415
NP_812128.1 BT_3216 None 132, 358
NP_812132.1 BT_3220 None 358, 451
NP_812185.1 BT_3273 None 349, 358
NP_812227.1 BT_3315 None 273, 415
NP_812302.1 BT_3390 None 156, 415
NP_812347.1 BT_3435 None 399, 415
NP_812354.1 BT_3442 None 415, 416
NP_812445.1 BT_3533 None 58, 358
NP_812446.1 BT_3534 None 87, 358
NP_812450.1 BT_3538 None 358, 428
NP_812552.1 BT_3641 None 228, 415
NP_812658.1 BT_3747 None 358, 415
NP_812735.1 BT_3824 None 373, 415
NP_812920.1 BT_4009 None 58, 415
NP_812981.1 BT_4070 None 9, 415
NP_812982.1 BT_4071 None 252, 415
NP_812984.1 BT_4073 None 399, 415
NP_813110.1 BT_4199 None 63, 415
NP_813139.1 BT_4228 None 263, 415
NP_813343.1 BT_4432 None 137, 358
NP_813403.1 BT_4492 None 358, 415
NP_813452.1 BT_4541 None 179, 358
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_810819.1
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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