Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_812194.1 BT_3282

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_812194.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_812194.1!

Warning: NP_812194.1 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
5826 9.00e-01 ctccTc.ttcgGGAAGaaggag
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5827 1.90e+04 AGttACtAC.GtTTt
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6026 4.00e+00 cGACtAacaAgcAa.AttcAGggA
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6027 3.70e+03 GCATcaggGCA
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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_812194.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_812194.1

NP_812194.1 has total of 50 gene neighbors in modules 50, 151
Gene neighbors (50)
Gene Common Name Description Module membership
NP_808942.1 BT_0029 None 151, 398
NP_808943.1 BT_0030 None 151, 398
NP_808944.1 BT_0031 None 7, 151
NP_808945.1 BT_0032 None 151, 315
NP_809049.1 BT_0136 None 50, 256
NP_810010.1 BT_1097 None 50, 356
NP_810085.1 BT_1172 None 151, 360
NP_810087.1 BT_1174 None 151, 406
NP_810351.1 BT_1438 None 144, 151
NP_810431.1 BT_1518 None 50, 450
NP_810432.1 BT_1519 None 50, 450
NP_810498.1 BT_1585 None 50, 149
NP_810551.1 BT_1638 None 151, 350
NP_810941.1 BT_2028 None 50, 450
NP_811033.1 BT_2120 None 50, 67
NP_811101.1 BT_2188 None 7, 50
NP_811234.1 BT_2321 None 151, 360
NP_811235.1 BT_2322 None 151, 360
NP_811252.1 BT_2339 None 7, 151
NP_811255.1 BT_2342 None 151, 356
NP_811291.1 BT_2378 None 50, 151
NP_811345.1 BT_2432 None 50, 415
NP_811592.1 BT_2680 None 50, 282
NP_811812.1 BT_2900 None 50, 252
NP_811897.1 BT_2985 None 50, 373
NP_811919.1 BT_3007 None 151, 158
NP_811950.1 BT_3038 None 50, 424
NP_811998.1 BT_3086 None 50, 235
NP_812053.1 BT_3141 None 151, 360
NP_812054.1 BT_3142 None 151, 360
NP_812055.1 BT_3143 None 151, 360
NP_812186.1 BT_3274 None 50, 349
NP_812187.1 BT_3275 None 50, 472
NP_812190.1 BT_3278 None 151, 284
NP_812191.1 BT_3279 None 50, 151
NP_812192.1 BT_3280 None 50, 151
NP_812193.1 BT_3281 None 50, 151
NP_812194.1 BT_3282 None 50, 151
NP_812329.1 BT_3417 None 50, 450
NP_812451.1 BT_3539 None 50, 252
NP_812457.1 BT_3545 None 16, 151
NP_812476.1 BT_3564 None 82, 151
NP_812792.1 BT_3881 None 7, 50
NP_813005.1 BT_4094 None 50, 288
NP_813144.1 BT_4233 None 50, 337
NP_813145.1 BT_4234 None 50, 337
NP_813346.1 BT_4435 None 151, 360
NP_813598.1 BT_4687 None 50, 252
NP_813641.1 BT_4730 None 50, 373
NP_813645.1 BT_4734 None 50, 256
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_812194.1
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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