Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_811149.1 BT_2236

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_811149.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_811149.1!

Warning: NP_811149.1 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
6568 1.50e-21 TAtcTTTGca..c..aaa
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6569 3.10e+00 GAAtAaaATTCaCcAaAtTaGCaC
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6592 1.30e-25 tagTAccTTTGC.gaa
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6593 1.10e+03 CagCgaAag.aaac
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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_811149.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_811149.1

NP_811149.1 has total of 60 gene neighbors in modules 428, 440
Gene neighbors (60)
Gene Common Name Description Module membership
NP_808921.1 BT_0008 None 323, 440
NP_809089.1 BT_0176 None 113, 440
NP_809145.1 BT_0232 None 126, 440
NP_809153.1 BT_0240 None 273, 428
NP_809332.1 BT_0419 None 361, 440
NP_809333.1 def None 361, 440
NP_809541.1 BT_0628 None 153, 440
NP_809610.1 BT_0697 None 184, 440
NP_809800.1 BT_0887 None 405, 428
NP_809883.1 BT_0970 None 156, 428
NP_810048.1 BT_1135 None 107, 440
NP_810061.1 BT_1148 None 221, 440
NP_810148.1 BT_1235 None 113, 440
NP_810222.1 BT_1309 None 382, 428
NP_810295.1 BT_1382 None 126, 440
NP_810494.1 BT_1581 None 323, 428
NP_810496.1 BT_1583 None 221, 440
NP_810526.1 BT_1613 None 125, 428
NP_810527.1 BT_1614 None 125, 428
NP_810746.1 BT_1833 None 184, 440
NP_810820.1 BT_1907 None 273, 428
NP_810891.1 ruvA None 361, 440
NP_811043.1 BT_2130 None 309, 428
NP_811052.1 BT_2139 None 210, 428
NP_811093.1 BT_2180 None 405, 428
NP_811100.1 BT_2187 None 113, 428
NP_811118.1 BT_2205 None 126, 440
NP_811149.1 BT_2236 None 428, 440
NP_811150.1 BT_2237 None 177, 440
NP_811161.1 BT_2248 None 153, 428
NP_811914.1 BT_3002 None 323, 428
NP_811915.1 BT_3003 None 372, 428
NP_811987.1 BT_3075 None 405, 428
NP_812061.1 BT_3149 None 405, 428
NP_812065.1 BT_3153 None 405, 428
NP_812181.1 BT_3269 None 126, 428
NP_812282.1 BT_3370 None 21, 440
NP_812314.1 BT_3402 None 54, 428
NP_812326.1 BT_3414 None 113, 440
NP_812342.1 rpsT None 125, 428
NP_812450.1 BT_3538 None 358, 428
NP_812551.1 BT_3640 None 412, 440
NP_812683.1 BT_3772 None 54, 440
NP_812712.1 BT_3801 None 177, 440
NP_812748.1 BT_3837 None 54, 440
NP_812838.1 BT_3927 None 184, 440
NP_812907.1 BT_3996 None 364, 428
NP_812908.1 BT_3997 None 96, 428
NP_812980.1 BT_4069 None 201, 428
NP_813095.1 BT_4184 None 126, 428
NP_813220.1 BT_4309 None 221, 440
NP_813324.1 BT_4413 None 308, 428
NP_813362.1 BT_4451 None 276, 440
NP_813388.1 BT_4477 None 126, 428
NP_813409.1 BT_4498 None 126, 440
NP_813426.1 BT_4515 None 63, 428
NP_813445.1 BT_4534 None 431, 440
NP_813462.1 trmE None 361, 440
NP_813512.1 BT_4601 None 54, 428
NP_813557.1 BT_4646 None 347, 428
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_811149.1
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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