Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_812662.1 BT_3751

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_812662.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_812662.1!

Warning: NP_812662.1 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
5822 8.30e+03 CCGGCaC
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5823 1.10e+04 TgTgTtTtTc
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5956 7.70e-01 T.ATAttgGtaGTatttTtaCg
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5957 1.10e+00 cTcttTtTTatgtgtcaaAgg
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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_812662.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_812662.1

NP_812662.1 has total of 41 gene neighbors in modules 47, 116
Gene neighbors (41)
Gene Common Name Description Module membership
NP_809667.1 BT_0754 None 29, 47
NP_809668.1 BT_0755 None 29, 47
NP_810430.1 BT_1517 None 47, 207
NP_810786.1 BT_1873 None 47, 278
NP_810787.1 BT_1874 None 47, 278
NP_810910.1 BT_1997 None 116, 373
NP_811020.1 BT_2107 None 47, 278
NP_811021.1 BT_2108 None 47, 278
NP_811022.1 BT_2109 None 47, 278
NP_811023.1 BT_2110 None 47, 278
NP_811370.1 BT_2457 None 47, 282
NP_811371.1 BT_2458 None 47, 282
NP_811372.1 BT_2459 None 47, 282
NP_811373.1 BT_2460 None 47, 143
NP_811374.1 BT_2461 None 47, 282
NP_811375.1 BT_2462 None 47, 282
NP_811833.1 BT_2921 None 116, 282
NP_811860.1 BT_2948 None 116, 204
NP_811861.1 BT_2949 None 116, 204
NP_811862.1 BT_2950 None 116, 204
NP_811863.1 BT_2951 None 116, 204
NP_811864.1 BT_2952 None 116, 204
NP_811865.1 BT_2953 None 116, 204
NP_811866.1 BT_2954 None 116, 204
NP_811867.1 BT_2955 None 116, 204
NP_811868.1 BT_2956 None 116, 204
NP_811869.1 BT_2957 None 116, 429
NP_812085.1 BT_3173 None 116, 178
NP_812660.1 BT_3749 None 47, 399
NP_812661.1 BT_3750 None 47, 116
NP_812662.1 BT_3751 None 47, 116
NP_812663.1 BT_3752 None 47, 116
NP_812664.1 BT_3753 None 47, 116
NP_812665.1 BT_3754 None 47, 116
NP_812863.1 BT_3952 None 116, 169
NP_813043.1 BT_4132 None 116, 252
NP_813044.1 BT_4133 None 116, 252
NP_813045.1 BT_4134 None 116, 252
NP_813046.1 BT_4135 None 116, 252
NP_813314.1 BT_4403 None 47, 209
NP_813345.1 BT_4434 None 15, 116
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_812662.1
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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