Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_809043.1 BT_0130

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_809043.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_809043.1!

Warning: NP_809043.1 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
5742 9.30e-01 gcCCtGTCaggC
Loader icon
5743 7.10e+03 TgGatGcGggg
Loader icon
5760 1.80e+04 CCGCCcCG
Loader icon
5761 2.40e+04 ctCcAca.gTc
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_809043.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_809043.1

NP_809043.1 has total of 58 gene neighbors in modules 7, 16
Gene neighbors (58)
Gene Common Name Description Module membership
NP_808944.1 BT_0031 None 7, 151
NP_809043.1 BT_0130 None 7, 16
NP_809143.1 BT_0230 None 16, 315
NP_809843.1 BT_0930 None 16, 121
NP_809866.1 BT_0953 None 16, 415
NP_809877.1 BT_0964 None 16, 398
NP_810049.1 BT_1136 None 16, 360
NP_810086.1 BT_1173 None 16, 149
NP_810103.1 BT_1190 None 16, 91
NP_810154.1 BT_1241 None 16, 149
NP_810158.1 BT_1245 None 7, 42
NP_810297.1 BT_1384 None 16, 60
NP_810298.1 BT_1385 None 16, 153
NP_810325.1 BT_1412 None 7, 14
NP_810339.1 BT_1426 None 16, 204
NP_810340.1 BT_1427 None 16, 45
NP_810378.1 BT_1465 None 7, 443
NP_810379.1 BT_1466 None 7, 149
NP_810381.1 BT_1468 None 7, 149
NP_810478.1 BT_1565 None 16, 406
NP_810497.1 BT_1584 None 16, 319
NP_810499.1 BT_1586 None 16, 319
NP_810554.1 BT_1641 None 16, 235
NP_810843.1 BT_1930 None 7, 119
NP_811014.1 BT_2101 None 16, 356
NP_811024.1 BT_2111 None 7, 443
NP_811025.1 BT_2112 None 7, 58
NP_811026.1 BT_2113 None 7, 263
NP_811097.1 BT_2184 None 7, 165
NP_811098.1 BT_2185 None 7, 165
NP_811101.1 BT_2188 None 7, 50
NP_811107.1 BT_2194 None 7, 73
NP_811108.1 BT_2195 None 7, 58
NP_811109.1 BT_2196 None 7, 73
NP_811227.1 BT_2314 None 16, 62
NP_811252.1 BT_2339 None 7, 151
NP_811289.1 BT_2376 None 7, 252
NP_811290.1 BT_2377 None 16, 356
NP_811368.1 BT_2455 None 15, 16
NP_811369.1 BT_2456 None 15, 16
NP_811589.1 BT_2677 None 16, 40
NP_811677.1 BT_2765 None 7, 91
NP_811707.1 BT_2795 None 7, 398
NP_812222.1 BT_3310 None 7, 288
NP_812223.1 BT_3311 None 7, 288
NP_812224.1 BT_3312 None 7, 288
NP_812225.1 BT_3313 None 7, 288
NP_812226.1 BT_3314 None 7, 288
NP_812426.1 BT_3514 None 16, 45
NP_812453.1 BT_3541 None 16, 169
NP_812457.1 BT_3545 None 16, 151
NP_812792.1 BT_3881 None 7, 50
NP_813182.1 BT_4271 None 7, 427
NP_813348.1 BT_4437 None 7, 119
NP_813527.1 BT_4616 None 16, 416
NP_813529.1 BT_4618 None 16, 325
NP_813603.1 BT_4692 None 4, 16
NP_813653.1 BT_4742 None 7, 398
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_809043.1
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