Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_812092.1 BT_3180

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_812092.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_812092.1!

Warning: NP_812092.1 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
6570 9.40e+05 TAtAtTtGCatatttAtaat
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6571 1.10e+04 TttTTctCtTT
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6622 8.00e+00 cTAatTTTGca
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6623 1.10e+02 cAttgaatgaaa.gAAAtctTCag
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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_812092.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_812092.1

NP_812092.1 has total of 60 gene neighbors in modules 429, 455
Gene neighbors (60)
Gene Common Name Description Module membership
NP_808997.1 BT_0084 None 67, 455
NP_809001.1 BT_0088 None 395, 455
NP_809002.1 BT_0089 None 395, 455
NP_809010.1 BT_0097 None 67, 455
NP_809040.1 BT_0127 None 4, 429
NP_809050.1 BT_0137 None 91, 455
NP_809178.1 BT_0265 None 42, 455
NP_809477.1 BT_0564 None 102, 429
NP_809671.1 BT_0758 None 429, 455
NP_809760.1 BT_0847 None 429, 472
NP_809846.1 BT_0933 None 136, 429
NP_809847.1 BT_0934 None 136, 429
NP_809918.1 BT_1005 None 319, 429
NP_809974.1 BT_1061 None 136, 429
NP_810034.1 BT_1121 None 443, 455
NP_810035.1 BT_1122 None 169, 455
NP_810232.1 BT_1319 None 355, 429
NP_810301.1 BT_1388 None 4, 429
NP_810310.1 BT_1397 None 73, 455
NP_810317.1 BT_1404 None 284, 429
NP_810343.1 BT_1430 None 429, 432
NP_810709.1 BT_1796 None 244, 429
NP_810788.1 BT_1875 None 278, 455
NP_811110.1 BT_2197 None 73, 429
NP_811132.1 BT_2219 None 308, 429
NP_811136.1 BT_2223 None 168, 429
NP_811248.1 BT_2335 None 67, 455
NP_811447.1 BT_2534 None 244, 429
NP_811487.1 BT_2574 None 102, 429
NP_811678.1 BT_2766 None 308, 429
NP_811687.1 BT_2775 None 235, 429
NP_811688.1 BT_2776 None 386, 429
NP_811704.1 BT_2792 None 398, 429
NP_811738.1 BT_2826 None 378, 429
NP_811802.1 BT_2890 None 206, 429
NP_811869.1 BT_2957 None 116, 429
NP_811877.1 BT_2965 None 415, 429
NP_811881.1 BT_2969 None 12, 455
NP_811882.1 BT_2970 None 263, 455
NP_811962.1 BT_3050 None 263, 455
NP_811970.1 BT_3058 None 308, 429
NP_812086.1 BT_3174 None 354, 455
NP_812087.1 BT_3175 None 365, 455
NP_812089.1 BT_3177 None 192, 455
NP_812090.1 BT_3178 None 192, 455
NP_812092.1 BT_3180 None 429, 455
NP_812120.1 BT_3208 None 282, 429
NP_812343.1 BT_3431 None 4, 429
NP_812893.1 BT_3982 None 158, 429
NP_812966.1 BT_4055 None 263, 455
NP_812967.1 BT_4056 None 263, 455
NP_813006.1 BT_4095 None 165, 429
NP_813026.1 BT_4115 None 235, 429
NP_813029.1 BT_4118 None 152, 429
NP_813073.1 BT_4162 None 91, 429
NP_813183.1 BT_4272 None 411, 429
NP_813320.1 BT_4409 None 198, 429
NP_813360.1 BT_4449 None 95, 455
NP_813479.1 BT_4568 None 455, 456
NP_813517.1 BT_4606 None 308, 429
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_812092.1
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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