Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_813513.1 BT_4602

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_813513.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_813513.1!

Warning: NP_813513.1 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
5842 1.20e+06 GTGTATATcTGaG
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5843 1.10e+01 aAaAA.AgaaAataA
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6424 1.80e+03 cTAacTTTGcA
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6425 5.50e+03 aAAaTgAgAag
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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_813513.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_813513.1

NP_813513.1 has total of 66 gene neighbors in modules 58, 356
Gene neighbors (66)
Gene Common Name Description Module membership
NP_809398.1 BT_0485 None 42, 356
NP_809465.1 BT_0552 None 58, 472
NP_809585.1 BT_0672 None 58, 206
NP_809665.1 BT_0752 None 58, 247
NP_809666.1 BT_0753 None 29, 58
NP_809751.1 BT_0838 None 58, 416
NP_809860.1 BT_0947 None 58, 169
NP_809878.1 BT_0965 None 58, 427
NP_810008.1 BT_1095 None 67, 356
NP_810009.1 BT_1096 None 308, 356
NP_810010.1 BT_1097 None 50, 356
NP_810174.1 BT_1261 None 58, 168
NP_810662.1 BT_1749 None 58, 308
NP_810685.1 BT_1772 None 58, 206
NP_810762.1 BT_1849 None 58, 152
NP_810818.1 BT_1905 None 58, 415
NP_811014.1 BT_2101 None 16, 356
NP_811025.1 BT_2112 None 7, 58
NP_811108.1 BT_2195 None 7, 58
NP_811112.1 BT_2199 None 29, 58
NP_811138.1 BT_2225 None 168, 356
NP_811255.1 BT_2342 None 151, 356
NP_811256.1 BT_2343 None 356, 358
NP_811258.1 BT_2345 None 144, 356
NP_811276.1 BT_2363 None 58, 235
NP_811290.1 BT_2377 None 16, 356
NP_811304.1 BT_2391 None 58, 261
NP_811349.1 BT_2436 None 58, 208
NP_811705.1 BT_2793 None 315, 356
NP_811706.1 BT_2794 None 315, 356
NP_811773.1 BT_2861 None 319, 356
NP_811775.1 BT_2863 None 82, 356
NP_811777.1 BT_2865 None 82, 356
NP_811778.1 BT_2866 None 356, 381
NP_811782.1 BT_2870 None 82, 356
NP_811783.1 BT_2871 None 82, 356
NP_811784.1 BT_2872 None 91, 356
NP_811785.1 BT_2873 None 82, 356
NP_811787.1 BT_2875 None 82, 356
NP_811788.1 BT_2876 None 82, 356
NP_811789.1 BT_2877 None 82, 356
NP_811792.1 BT_2880 None 82, 356
NP_811793.1 BT_2881 None 82, 356
NP_811880.1 BT_2968 None 58, 354
NP_811899.1 BT_2987 None 91, 356
NP_811900.1 BT_2988 None 315, 356
NP_811901.1 BT_2989 None 315, 356
NP_811940.1 BT_3028 None 58, 288
NP_811954.1 BT_3042 None 356, 416
NP_812010.1 BT_3098 None 58, 261
NP_812011.1 BT_3099 None 91, 356
NP_812021.1 BT_3109 None 58, 60
NP_812043.1 BT_3131 None 58, 427
NP_812067.1 BT_3155 None 58, 277
NP_812290.1 BT_3378 None 198, 356
NP_812378.1 BT_3466 None 99, 356
NP_812435.1 BT_3523 None 29, 58
NP_812445.1 BT_3533 None 58, 358
NP_812920.1 BT_4009 None 58, 415
NP_813054.1 BT_4143 None 120, 356
NP_813185.1 BT_4274 None 263, 356
NP_813308.1 BT_4397 None 315, 356
NP_813309.1 BT_4398 None 315, 356
NP_813353.1 BT_4442 None 45, 58
NP_813421.1 BT_4510 None 58, 91
NP_813513.1 BT_4602 None 58, 356
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_813513.1
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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