Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_812988.1 BT_4077

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_812988.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_812988.1!

Warning: NP_812988.1 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
5870 8.60e-03 AaAag.TaaAAaaaAGA.tgT.TT
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5871 3.70e+01 AtCctcgATTGtGcaaatAATtTC
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6526 3.60e+02 tttagtTaAAaAcagAaAAA
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6527 1.40e+04 CTtTTTta
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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_812988.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_812988.1

NP_812988.1 has total of 55 gene neighbors in modules 73, 407
Gene neighbors (55)
Gene Common Name Description Module membership
NP_809042.1 BT_0129 None 42, 407
NP_809052.1 BT_0139 None 263, 407
NP_809053.1 BT_0140 None 278, 407
NP_809054.1 BT_0141 None 278, 407
NP_809055.1 BT_0142 None 278, 407
NP_809057.1 BT_0144 None 23, 407
NP_809175.1 BT_0262 None 60, 407
NP_809576.1 BT_0663 None 45, 407
NP_809577.1 BT_0664 None 45, 407
NP_810307.1 BT_1394 None 73, 112
NP_810308.1 BT_1395 None 73, 112
NP_810310.1 BT_1397 None 73, 455
NP_810311.1 BT_1398 None 73, 112
NP_810312.1 BT_1399 None 73, 112
NP_810313.1 BT_1400 None 73, 112
NP_810656.1 BT_1743 None 97, 407
NP_810686.1 BT_1773 None 73, 192
NP_810687.1 BT_1774 None 73, 456
NP_810700.1 BT_1787 None 283, 407
NP_810701.1 BT_1788 None 283, 407
NP_810779.1 BT_1866 None 9, 407
NP_810895.1 BT_1982 None 263, 407
NP_811105.1 BT_2192 None 73, 450
NP_811106.1 BT_2193 None 73, 450
NP_811107.1 BT_2194 None 7, 73
NP_811109.1 BT_2196 None 7, 73
NP_811110.1 BT_2197 None 73, 429
NP_811682.1 BT_2770 None 73, 472
NP_811683.1 BT_2771 None 73, 91
NP_811684.1 BT_2772 None 63, 73
NP_811685.1 BT_2773 None 63, 73
NP_811686.1 BT_2774 None 73, 443
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_812013.1 BT_3101 None 259, 407
NP_812018.1 BT_3106 None 259, 407
NP_812019.1 BT_3107 None 278, 407
NP_812020.1 BT_3108 None 278, 407
NP_812068.1 BT_3156 None 29, 73
NP_812986.1 BT_4075 None 256, 407
NP_812987.1 BT_4076 None 73, 368
NP_812988.1 BT_4077 None 73, 407
NP_812989.1 BT_4078 None 278, 407
NP_812990.1 BT_4079 None 278, 407
NP_812996.1 BT_4085 None 256, 407
NP_812997.1 BT_4086 None 256, 407
NP_812998.1 BT_4087 None 256, 407
NP_812999.1 BT_4088 None 256, 407
NP_813000.1 BT_4089 None 256, 407
NP_813001.1 BT_4090 None 256, 407
NP_813002.1 BT_4091 None 73, 407
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_812988.1
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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