Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_811996.1 BT_3084

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_811996.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_811996.1!

Warning: NP_811996.1 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
5830 1.20e-01 aaaaAt.gagaAtcAagTATTaTc
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5831 2.00e+03 gacAAAtAtAg
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5874 4.10e-05 aaaatgcttAtaTTTGtag.
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5875 7.40e+03 GGGGGCaCTTG
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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_811996.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_811996.1

NP_811996.1 has total of 43 gene neighbors in modules 52, 75
Gene neighbors (43)
Gene Common Name Description Module membership
NP_809235.1 BT_0322 None 22, 75
NP_809248.1 BT_0335 None 75, 253
NP_809603.1 BT_0690 None 75, 102
NP_809606.1 BT_0693 None 52, 444
NP_809607.1 BT_0694 None 52, 444
NP_809608.1 BT_0695 None 52, 444
NP_810546.1 BT_1633 None 75, 328
NP_810955.1 BT_2042 None 75, 218
NP_811266.1 BT_2353 None 52, 363
NP_811318.1 BT_2405 None 75, 152
NP_811319.1 BT_2406 None 75, 328
NP_811320.1 BT_2407 None 75, 444
NP_811352.1 BT_2439 None 75, 227
NP_811433.1 BT_2520 None 75, 348
NP_811458.1 BT_2545 None 75, 379
NP_811993.1 BT_3081 None 52, 448
NP_811995.1 BT_3083 None 75, 445
NP_811996.1 BT_3084 None 52, 75
NP_812097.1 BT_3185 None 75, 198
NP_812129.1 BT_3217 None 52, 363
NP_812130.1 BT_3218 None 52, 363
NP_812176.1 BT_3264 None 52, 94
NP_812177.1 BT_3265 None 52, 94
NP_812178.1 BT_3266 None 43, 75
NP_812217.1 BT_3305 None 52, 372
NP_812218.1 BT_3306 None 75, 239
NP_812283.1 BT_3371 None 21, 52
NP_812293.1 BT_3381 None 52, 201
NP_812294.1 BT_3382 None 52, 201
NP_812295.1 BT_3383 None 52, 201
NP_812373.1 dut None 52, 364
NP_812374.1 BT_3462 None 52, 65
NP_812375.1 BT_3463 None 52, 65
NP_812377.1 BT_3465 None 52, 201
NP_812470.1 BT_3558 None 52, 363
NP_812471.1 BT_3559 None 52, 363
NP_812472.1 BT_3560 None 52, 363
NP_812473.1 BT_3561 None 52, 363
NP_812474.1 BT_3562 None 52, 363
NP_812475.1 BT_3563 None 52, 363
NP_813140.1 BT_4229 None 75, 253
NP_813408.1 BT_4497 None 75, 376
NP_813537.1 BT_4626 None 75, 301
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_811996.1
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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