Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_813414.1 BT_4503

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_813414.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_813414.1!

Warning: NP_813414.1 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
5756 1.90e-11 TAtaTTTGCc.
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5757 1.40e+02 AAaaAtgt.TatcTTTGtgct
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6102 6.90e+02 aAAaaaTAgcTTtTTtaT
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6103 5.90e+03 CAAagatAcAAAAta
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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_813414.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_813414.1

NP_813414.1 has total of 53 gene neighbors in modules 14, 189
Gene neighbors (53)
Gene Common Name Description Module membership
NP_809082.1 BT_0169 None 189, 432
NP_809173.1 BT_0260 None 189, 274
NP_809174.1 BT_0261 None 189, 274
NP_809548.1 BT_0635 None 14, 68
NP_809554.1 BT_0641 None 177, 189
NP_809558.1 BT_0645 None 14, 187
NP_809724.1 BT_0811 None 14, 156
NP_809766.1 BT_0853 None 14, 96
NP_809781.1 BT_0868 None 189, 314
NP_809782.1 BT_0869 None 189, 371
NP_809841.1 BT_0928 None 14, 68
NP_809844.1 BT_0931 None 14, 261
NP_809882.1 BT_0969 None 96, 189
NP_809984.1 BT_1071 None 14, 431
NP_810084.1 BT_1171 None 14, 124
NP_810230.1 BT_1317 None 170, 189
NP_810250.1 BT_1337 None 189, 322
NP_810325.1 BT_1412 None 7, 14
NP_810326.1 BT_1413 None 14, 68
NP_810473.1 BT_1560 None 14, 24
NP_810475.1 BT_1562 None 14, 405
NP_810810.1 BT_1897 None 63, 189
NP_810811.1 BT_1898 None 189, 208
NP_810834.1 BT_1921 None 14, 124
NP_810964.1 BT_2051 None 14, 309
NP_811006.1 BT_2093 None 189, 314
NP_811102.1 BT_2189 None 6, 189
NP_811151.1 BT_2238 None 14, 152
NP_811155.1 BT_2242 None 14, 314
NP_811194.1 BT_2281 None 189, 221
NP_811282.1 BT_2369 None 68, 189
NP_811492.1 BT_2579 None 14, 51
NP_811563.1 BT_2650 None 68, 189
NP_811673.1 BT_2761 None 14, 124
NP_811873.1 BT_2961 None 14, 124
NP_811922.1 BT_3010 None 14, 189
NP_812325.1 BT_3413 None 14, 187
NP_812429.1 BT_3517 None 14, 189
NP_812461.1 BT_3549 None 14, 187
NP_812468.1 BT_3556 None 177, 189
NP_812607.1 BT_3696 None 189, 338
NP_813038.1 nagB None 14, 273
NP_813123.1 BT_4212 None 177, 189
NP_813133.1 BT_4222 None 96, 189
NP_813249.1 BT_4338 None 14, 187
NP_813266.1 BT_4355 None 189, 432
NP_813414.1 BT_4503 None 14, 189
NP_813420.1 BT_4509 None 189, 404
NP_813547.1 BT_4636 None 14, 273
NP_813585.1 BT_4674 None 189, 314
NP_813608.1 BT_4697 None 14, 301
NP_813666.1 BT_4755 None 14, 431
NP_813667.1 BT_4756 None 14, 38
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_813414.1
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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