Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_809876.1 BT_0963

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_809876.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_809876.1!

Warning: NP_809876.1 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
5948 5.50e-01 gTAaAAat.TCcGtAAtTcaTctA
Loader icon
5949 1.00e+03 TCAAaTCc.TCA.AAT
Loader icon
6602 9.80e+02 cTAtcTTtGcA
Loader icon
6603 2.10e+04 CCTGCC
Loader icon
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_809876.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_809876.1

NP_809876.1 has total of 40 gene neighbors in modules 112, 445
Gene neighbors (40)
Gene Common Name Description Module membership
NP_809068.1 trmU None 109, 445
NP_809182.1 BT_0269 None 110, 112
NP_809183.1 BT_0270 None 110, 112
NP_809184.1 BT_0271 None 110, 112
NP_809186.1 BT_0273 None 110, 112
NP_809187.1 BT_0274 None 110, 112
NP_809188.1 BT_0275 None 110, 112
NP_809189.1 BT_0276 None 110, 112
NP_809190.1 BT_0277 None 110, 112
NP_809191.1 BT_0278 None 110, 112
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_809604.1 BT_0691 None 109, 445
NP_809605.1 BT_0692 None 109, 445
NP_809872.1 BT_0959 None 112, 384
NP_809873.1 BT_0960 None 112, 384
NP_809874.1 BT_0961 None 112, 384
NP_809875.1 BT_0962 None 112, 384
NP_809876.1 BT_0963 None 112, 445
NP_810307.1 BT_1394 None 73, 112
NP_810308.1 BT_1395 None 73, 112
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_810316.1 BT_1403 None 112, 445
NP_810320.1 BT_1407 None 109, 445
NP_810808.1 BT_1895 None 150, 445
NP_810809.1 BT_1896 None 150, 445
NP_810911.1 BT_1998 None 157, 445
NP_810912.1 BT_1999 None 157, 445
NP_811353.1 BT_2440 None 328, 445
NP_811354.1 BT_2441 None 124, 445
NP_811457.1 BT_2544 None 156, 445
NP_811844.1 BT_2932 None 127, 445
NP_811992.1 BT_3080 None 413, 445
NP_811995.1 BT_3083 None 75, 445
NP_811997.1 BT_3085 None 152, 445
NP_813365.1 BT_4454 None 376, 445
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_809876.1
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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