Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_810831.1 BT_1918

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_810831.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_810831.1!

Warning: NP_810831.1 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
5790 9.20e+02 aAtcagataGGggtaa.cGtA
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5791 4.80e+03 GCCGAC
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6006 4.80e-02 attTattatcTTTGC
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6007 1.10e+04 GCCACCGC
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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_810831.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_810831.1

NP_810831.1 has total of 44 gene neighbors in modules 31, 141
Gene neighbors (44)
Gene Common Name Description Module membership
NP_809036.1 BT_0123 None 31, 223
NP_809037.1 BT_0124 None 31, 141
NP_809038.1 BT_0125 None 31, 141
NP_809198.1 BT_0285 None 112, 141
NP_809199.1 BT_0286 None 112, 141
NP_809200.1 BT_0287 None 112, 141
NP_809201.1 BT_0288 None 112, 141
NP_809557.1 BT_0644 None 141, 290
NP_810105.1 BT_1192 None 141, 290
NP_810173.1 BT_1260 None 141, 168
NP_810520.1 BT_1607 None 141, 444
NP_810521.1 BT_1608 None 31, 141
NP_810537.1 BT_1624 None 31, 88
NP_810548.1 BT_1635 None 141, 208
NP_810683.1 BT_1770 None 141, 378
NP_810690.1 BT_1777 None 141, 205
NP_810831.1 BT_1918 None 31, 141
NP_811059.1 BT_2146 None 141, 290
NP_811575.1 BT_2662 None 141, 444
NP_811694.1 BT_2782 None 141, 290
NP_811695.1 BT_2783 None 141, 290
NP_811715.1 BT_2803 None 31, 66
NP_811716.1 BT_2804 None 31, 66
NP_811717.1 BT_2805 None 31, 66
NP_811718.1 BT_2806 None 31, 66
NP_811719.1 BT_2807 None 31, 66
NP_811720.1 BT_2808 None 31, 66
NP_811721.1 BT_2809 None 31, 66
NP_811764.1 BT_2852 None 141, 205
NP_811924.1 BT_3012 None 31, 401
NP_811925.1 BT_3013 None 31, 401
NP_811926.1 BT_3014 None 31, 401
NP_811927.1 BT_3015 None 31, 401
NP_812081.1 BT_3169 None 31, 77
NP_812084.1 BT_3172 None 141, 164
NP_812214.1 BT_3302 None 141, 444
NP_812252.1 BT_3340 None 128, 141
NP_812379.1 BT_3467 None 88, 141
NP_812428.1 BT_3516 None 141, 156
NP_812619.1 BT_3708 None 141, 298
NP_812678.1 BT_3767 None 88, 141
NP_812711.1 BT_3800 None 77, 141
NP_812965.1 BT_4054 None 88, 141
NP_813625.1 BT_4714 None 141, 448
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_810831.1
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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