Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_811443.1 BT_2530

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_811443.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_811443.1!

Warning: NP_811443.1 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
5758 1.30e-01 a.CaTtgCtCcC.ct
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5759 6.80e+02 AcAAgTtcTAatTcCcCctcC
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5992 1.20e-18 gtaaGcCcccGataaagt..ccg
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5993 2.60e-10 tTTtttcgcTcgatctTTgcc
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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_811443.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_811443.1

NP_811443.1 has total of 52 gene neighbors in modules 15, 134
Gene neighbors (52)
Gene Common Name Description Module membership
NP_809176.1 BT_0263 None 15, 60
NP_809195.1 BT_0282 None 15, 284
NP_809317.1 BT_0404 None 15, 140
NP_809318.1 BT_0405 None 15, 140
NP_810033.1 BT_1120 None 15, 97
NP_810101.1 BT_1188 None 15, 319
NP_810102.1 BT_1189 None 15, 319
NP_810235.1 BT_1322 None 15, 447
NP_810305.1 BT_1392 None 15, 256
NP_810619.1 BT_1706 None 15, 97
NP_811134.1 BT_2221 None 15, 308
NP_811140.1 BT_2227 None 134, 190
NP_811179.1 BT_2266 None 15, 308
NP_811211.1 BT_2298 None 134, 385
NP_811212.1 BT_2299 None 134, 385
NP_811213.1 BT_2300 None 134, 385
NP_811214.1 BT_2301 None 134, 385
NP_811215.1 BT_2302 None 134, 385
NP_811216.1 BT_2303 None 134, 385
NP_811260.1 BT_2347 None 134, 190
NP_811261.1 BT_2348 None 134, 190
NP_811263.1 BT_2350 None 134, 190
NP_811264.1 BT_2351 None 134, 190
NP_811355.1 BT_2442 None 15, 45
NP_811356.1 BT_2443 None 15, 406
NP_811358.1 BT_2445 None 134, 450
NP_811368.1 BT_2455 None 15, 16
NP_811369.1 BT_2456 None 15, 16
NP_811383.1 BT_2470 None 15, 45
NP_811384.1 BT_2471 None 15, 45
NP_811443.1 BT_2530 None 15, 134
NP_811444.1 BT_2531 None 134, 176
NP_811445.1 BT_2532 None 119, 134
NP_811446.1 BT_2533 None 134, 176
NP_811572.1 BT_2659 None 15, 450
NP_811573.1 BT_2660 None 15, 450
NP_811574.1 BT_2661 None 15, 60
NP_811842.1 BT_2930 None 134, 415
NP_811843.1 BT_2931 None 134, 145
NP_812405.1 BT_3493 None 15, 330
NP_812927.1 BT_4016 None 12, 134
NP_812928.1 BT_4017 None 12, 134
NP_813052.1 BT_4141 None 15, 472
NP_813186.1 BT_4275 None 134, 190
NP_813345.1 BT_4434 None 15, 116
NP_813354.1 BT_4443 None 15, 45
NP_813355.1 BT_4444 None 15, 45
NP_813436.1 BT_4525 None 15, 60
NP_813514.1 BT_4603 None 15, 308
NP_813515.1 BT_4604 None 15, 45
NP_813516.1 BT_4605 None 15, 308
NP_813597.1 BT_4686 None 99, 134
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_811443.1
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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