Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_809040.1 BT_0127

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_809040.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_809040.1!

Warning: NP_809040.1 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
5736 5.70e+02 g.GcAAAa.tACaa
Loader icon
5737 2.90e+02 CttctttctGCaaA.cat.c
Loader icon
6570 9.40e+05 TAtAtTtGCatatttAtaat
Loader icon
6571 1.10e+04 TttTTctCtTT
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_809040.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_809040.1

NP_809040.1 has total of 57 gene neighbors in modules 4, 429
Gene neighbors (57)
Gene Common Name Description Module membership
NP_809040.1 BT_0127 None 4, 429
NP_809249.1 BT_0336 None 4, 102
NP_809250.1 BT_0337 None 4, 102
NP_809477.1 BT_0564 None 102, 429
NP_809508.1 BT_0595 None 4, 102
NP_809546.1 BT_0633 None 4, 133
NP_809547.1 BT_0634 None 4, 133
NP_809594.1 BT_0681 None 4, 235
NP_809645.1 BT_0732 None 4, 91
NP_809671.1 BT_0758 None 429, 455
NP_809674.1 BT_0761 None 4, 53
NP_809760.1 BT_0847 None 429, 472
NP_809830.1 BT_0917 None 4, 244
NP_809846.1 BT_0933 None 136, 429
NP_809847.1 BT_0934 None 136, 429
NP_809885.1 BT_0972 None 4, 53
NP_809918.1 BT_1005 None 319, 429
NP_809974.1 BT_1061 None 136, 429
NP_810100.1 BT_1187 None 4, 126
NP_810232.1 BT_1319 None 355, 429
NP_810301.1 BT_1388 None 4, 429
NP_810317.1 BT_1404 None 284, 429
NP_810343.1 BT_1430 None 429, 432
NP_810570.1 BT_1657 None 4, 308
NP_810709.1 BT_1796 None 244, 429
NP_810844.1 BT_1931 None 4, 253
NP_811110.1 BT_2197 None 73, 429
NP_811132.1 BT_2219 None 308, 429
NP_811136.1 BT_2223 None 168, 429
NP_811154.1 BT_2241 None 4, 198
NP_811447.1 BT_2534 None 244, 429
NP_811487.1 BT_2574 None 102, 429
NP_811678.1 BT_2766 None 308, 429
NP_811687.1 BT_2775 None 235, 429
NP_811688.1 BT_2776 None 386, 429
NP_811704.1 BT_2792 None 398, 429
NP_811738.1 BT_2826 None 378, 429
NP_811802.1 BT_2890 None 206, 429
NP_811869.1 BT_2957 None 116, 429
NP_811877.1 BT_2965 None 415, 429
NP_811970.1 BT_3058 None 308, 429
NP_812092.1 BT_3180 None 429, 455
NP_812120.1 BT_3208 None 282, 429
NP_812196.1 BT_3284 None 4, 277
NP_812202.1 BT_3290 None 4, 87
NP_812343.1 BT_3431 None 4, 429
NP_812893.1 BT_3982 None 158, 429
NP_813006.1 BT_4095 None 165, 429
NP_813026.1 BT_4115 None 235, 429
NP_813029.1 BT_4118 None 152, 429
NP_813073.1 BT_4162 None 91, 429
NP_813183.1 BT_4272 None 411, 429
NP_813320.1 BT_4409 None 198, 429
NP_813496.1 BT_4585 None 4, 472
NP_813517.1 BT_4606 None 308, 429
NP_813586.1 BT_4675 None 4, 198
NP_813603.1 BT_4692 None 4, 16
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_809040.1
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