Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_812967.1 BT_4056

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_812967.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_812967.1!

Warning: NP_812967.1 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
6250 8.50e-05 GCAAAaaTAag
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6251 7.00e+02 TTgAa.agct.a.aAaaaATacgc
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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_812967.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_812967.1

NP_812967.1 has total of 46 gene neighbors in modules 263, 455
Gene neighbors (46)
Gene Common Name Description Module membership
NP_808920.1 BT_0007 None 190, 263
NP_808938.1 BT_0025 None 169, 263
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_809050.1 BT_0137 None 91, 455
NP_809052.1 BT_0139 None 263, 407
NP_809178.1 BT_0265 None 42, 455
NP_809179.1 BT_0266 None 252, 263
NP_809578.1 BT_0665 None 91, 263
NP_809579.1 BT_0666 None 45, 263
NP_809580.1 BT_0667 None 45, 263
NP_809671.1 BT_0758 None 429, 455
NP_809762.1 BT_0849 None 97, 263
NP_809763.1 BT_0850 None 97, 263
NP_810034.1 BT_1121 None 443, 455
NP_810035.1 BT_1122 None 169, 455
NP_810310.1 BT_1397 None 73, 455
NP_810788.1 BT_1875 None 278, 455
NP_810803.1 BT_1890 None 46, 263
NP_810894.1 BT_1981 None 263, 472
NP_810895.1 BT_1982 None 263, 407
NP_811026.1 BT_2113 None 7, 263
NP_811248.1 BT_2335 None 67, 455
NP_811427.1 BT_2514 None 236, 263
NP_811881.1 BT_2969 None 12, 455
NP_811882.1 BT_2970 None 263, 455
NP_811928.1 BT_3016 None 40, 263
NP_811929.1 BT_3017 None 40, 263
NP_811962.1 BT_3050 None 263, 455
NP_812036.1 BT_3124 None 235, 263
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_812233.1 BT_3321 None 42, 263
NP_812966.1 BT_4055 None 263, 455
NP_812967.1 BT_4056 None 263, 455
NP_813047.1 BT_4136 None 252, 263
NP_813139.1 BT_4228 None 263, 415
NP_813185.1 BT_4274 None 263, 356
NP_813312.1 BT_4401 None 263, 315
NP_813360.1 BT_4449 None 95, 455
NP_813479.1 BT_4568 None 455, 456
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_812967.1
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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