Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_811287.1 BT_2374

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_811287.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_811287.1!

Warning: NP_811287.1 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
5836 6.50e+03 GAAaCA
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5837 3.40e+04 AACAaAGGT
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6140 6.60e-06 ttTAtcTTTGt
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6141 5.50e+04 TGtTgTATTgaGgcaaaAaaa.AG
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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_811287.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_811287.1

NP_811287.1 has total of 60 gene neighbors in modules 55, 208
Gene neighbors (60)
Gene Common Name Description Module membership
NP_809019.1 BT_0106 None 78, 208
NP_809051.1 BT_0138 None 208, 444
NP_809208.1 BT_0295 None 6, 208
NP_809479.1 BT_0566 None 55, 322
NP_809480.1 BT_0567 None 55, 322
NP_809493.1 BT_0580 None 55, 264
NP_809601.1 BT_0688 None 55, 102
NP_809602.1 BT_0689 None 55, 264
NP_809615.1 BT_0702 None 55, 264
NP_809859.1 BT_0946 None 208, 322
NP_809917.1 BT_1004 None 117, 208
NP_809964.1 BT_1051 None 208, 322
NP_810056.1 BT_1143 None 208, 438
NP_810104.1 BT_1191 None 208, 403
NP_810112.1 BT_1199 None 55, 264
NP_810146.1 BT_1233 None 208, 378
NP_810185.1 BT_1272 None 208, 233
NP_810321.1 BT_1408 None 55, 264
NP_810322.1 BT_1409 None 55, 264
NP_810323.1 BT_1410 None 55, 264
NP_810354.1 BT_1441 None 208, 411
NP_810530.1 BT_1617 None 168, 208
NP_810548.1 BT_1635 None 141, 208
NP_810682.1 BT_1769 None 55, 91
NP_810738.1 BT_1825 None 63, 208
NP_810811.1 BT_1898 None 189, 208
NP_811111.1 BT_2198 None 117, 208
NP_811117.1 BT_2204 None 208, 261
NP_811124.1 BT_2211 None 55, 264
NP_811125.1 BT_2212 None 55, 264
NP_811126.1 BT_2213 None 55, 264
NP_811127.1 BT_2214 None 55, 264
NP_811128.1 BT_2215 None 55, 264
NP_811286.1 BT_2373 None 55, 227
NP_811287.1 BT_2374 None 55, 208
NP_811349.1 BT_2436 None 58, 208
NP_811662.1 BT_2750 None 208, 235
NP_811933.1 BT_3021 None 87, 208
NP_811935.1 BT_3023 None 208, 322
NP_812459.1 BT_3547 None 208, 308
NP_812492.1 BT_3581 None 55, 329
NP_812493.1 BT_3582 None 55, 165
NP_812494.1 BT_3583 None 55, 329
NP_812495.1 BT_3584 None 55, 329
NP_812496.1 BT_3585 None 208, 329
NP_812497.1 BT_3586 None 208, 444
NP_812556.1 BT_3645 None 208, 363
NP_812659.1 BT_3748 None 208, 261
NP_812679.1 BT_3768 None 208, 322
NP_812796.1 BT_3885 None 55, 430
NP_812862.1 BT_3951 None 77, 208
NP_813090.1 BT_4179 None 208, 288
NP_813105.1 BT_4194 None 208, 219
NP_813106.1 BT_4195 None 208, 219
NP_813131.1 BT_4220 None 55, 322
NP_813235.1 BT_4324 None 55, 430
NP_813236.1 BT_4325 None 55, 430
NP_813237.1 BT_4326 None 55, 430
NP_813307.1 BT_4396 None 208, 322
NP_813616.1 BT_4705 None 208, 261
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_811287.1
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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