Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_809667.1 BT_0754

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_809667.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_809667.1!

Warning: NP_809667.1 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
5786 1.80e+02 agtTtTCccccg.acTtac
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5787 3.50e+03 AgAggAaAGaA
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5822 8.30e+03 CCGGCaC
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5823 1.10e+04 TgTgTtTtTc
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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_809667.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_809667.1

NP_809667.1 has total of 51 gene neighbors in modules 29, 47
Gene neighbors (51)
Gene Common Name Description Module membership
NP_809666.1 BT_0753 None 29, 58
NP_809667.1 BT_0754 None 29, 47
NP_809668.1 BT_0755 None 29, 47
NP_810382.1 BT_1469 None 29, 164
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_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_811112.1 BT_2199 None 29, 58
NP_811113.1 BT_2200 None 29, 192
NP_811114.1 BT_2201 None 29, 192
NP_811116.1 BT_2203 None 29, 164
NP_811363.1 BT_2450 None 29, 110
NP_811364.1 BT_2451 None 29, 110
NP_811365.1 BT_2452 None 29, 110
NP_811366.1 BT_2453 None 29, 110
NP_811367.1 BT_2454 None 29, 110
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_812068.1 BT_3156 None 29, 73
NP_812070.1 BT_3158 None 29, 205
NP_812071.1 BT_3159 None 29, 205
NP_812435.1 BT_3523 None 29, 58
NP_812499.1 BT_3588 None 29, 165
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_812869.1 BT_3958 None 29, 452
NP_812870.1 BT_3959 None 29, 452
NP_812871.1 BT_3960 None 29, 452
NP_812872.1 BT_3961 None 29, 452
NP_812873.1 BT_3962 None 29, 452
NP_812874.1 BT_3963 None 29, 452
NP_812875.1 BT_3964 None 29, 452
NP_812876.1 BT_3965 None 29, 452
NP_813314.1 BT_4403 None 47, 209
NP_813635.1 BT_4724 None 29, 164
NP_813636.1 BT_4725 None 29, 164
NP_813637.1 BT_4726 None 29, 164
NP_813638.1 BT_4727 None 29, 164
NP_813639.1 BT_4728 None 29, 164
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_809667.1
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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