Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_811428.1 BT_2515

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_811428.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_811428.1!

Warning: NP_811428.1 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
5966 5.90e-04 aagacttc.aCCtt.ca.tctaC
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5967 2.80e+03 AAaCgGAAtGc
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6364 3.50e-03 TGtGCgT.taTGcAC
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6365 5.80e+01 GgtTGatcGccaaCaG.cgcC
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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_811428.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_811428.1

NP_811428.1 has total of 47 gene neighbors in modules 121, 325
Gene neighbors (47)
Gene Common Name Description Module membership
NP_808916.1 BT_0003 None 325, 373
NP_808930.1 BT_0017 None 267, 325
NP_808946.1 BT_0033 None 325, 398
NP_809316.1 BT_0403 None 283, 325
NP_809709.1 BT_0796 None 325, 373
NP_809711.1 BT_0798 None 241, 325
NP_809764.1 BT_0851 None 121, 406
NP_809765.1 BT_0852 None 121, 395
NP_809770.1 BT_0857 None 325, 368
NP_809771.1 BT_0858 None 325, 368
NP_809772.1 BT_0859 None 325, 368
NP_809775.1 BT_0862 None 325, 368
NP_809776.1 BT_0863 None 325, 368
NP_809777.1 BT_0864 None 325, 368
NP_809843.1 BT_0930 None 16, 121
NP_809913.1 BT_1000 None 315, 325
NP_810429.1 BT_1516 None 99, 325
NP_810822.1 BT_1909 None 325, 434
NP_811195.1 BT_2282 None 121, 385
NP_811196.1 BT_2283 None 121, 385
NP_811197.1 BT_2284 None 121, 385
NP_811198.1 BT_2285 None 121, 385
NP_811199.1 BT_2286 None 121, 385
NP_811257.1 BT_2344 None 121, 190
NP_811357.1 BT_2444 None 121, 395
NP_811380.1 BT_2467 None 99, 121
NP_811428.1 BT_2515 None 121, 325
NP_811794.1 BT_2882 None 121, 381
NP_811795.1 BT_2883 None 121, 145
NP_811796.1 BT_2884 None 121, 145
NP_811797.1 BT_2885 None 121, 145
NP_811874.1 BT_2962 None 121, 192
NP_811875.1 BT_2963 None 121, 192
NP_811876.1 BT_2964 None 121, 192
NP_811892.1 BT_2980 None 40, 325
NP_811905.1 BT_2993 None 121, 453
NP_811906.1 BT_2994 None 121, 319
NP_811907.1 BT_2995 None 12, 121
NP_811974.1 BT_3062 None 121, 267
NP_812228.1 BT_3316 None 45, 121
NP_812776.1 BT_3865 None 190, 325
NP_813432.1 BT_4521 None 121, 319
NP_813528.1 BT_4617 None 267, 325
NP_813529.1 BT_4618 None 16, 325
NP_813530.1 BT_4619 None 325, 381
NP_813676.1 BT_4765 None 176, 325
NP_813677.1 BT_4766 None 99, 325
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_811428.1
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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