Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_813007.1 BT_4096

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_813007.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_813007.1!

Warning: NP_813007.1 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
6036 3.70e+02 ATaTTTGc
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6037 1.10e+03 AAACTaAccATTcTActtCCaT
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6194 2.70e+03 GCTgccgtaTttaTCcCCgg
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6195 2.40e+04 CCgACGGC
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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_813007.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_813007.1

NP_813007.1 has total of 61 gene neighbors in modules 156, 235
Gene neighbors (61)
Gene Common Name Description Module membership
NP_808941.1 BT_0028 None 206, 235
NP_809331.1 BT_0418 None 156, 353
NP_809418.1 BT_0505 None 156, 242
NP_809496.1 BT_0583 None 126, 235
NP_809537.1 BT_0624 None 68, 156
NP_809594.1 BT_0681 None 4, 235
NP_809724.1 BT_0811 None 14, 156
NP_809840.1 BT_0927 None 68, 156
NP_809883.1 BT_0970 None 156, 428
NP_809895.1 BT_0982 None 235, 415
NP_809927.1 BT_1014 None 97, 235
NP_810047.1 BT_1134 None 53, 235
NP_810051.1 BT_1138 None 156, 273
NP_810167.1 BT_1254 None 156, 157
NP_810199.1 BT_1286 None 235, 416
NP_810373.1 BT_1460 None 138, 235
NP_810507.1 BT_1594 None 235, 305
NP_810524.1 BT_1611 None 206, 235
NP_810529.1 BT_1616 None 53, 235
NP_810554.1 BT_1641 None 16, 235
NP_810689.1 BT_1776 None 156, 168
NP_810784.1 BT_1871 None 53, 235
NP_810785.1 BT_1872 None 53, 235
NP_810842.1 BT_1929 None 235, 450
NP_810900.1 BT_1987 None 235, 416
NP_810940.1 BT_2027 None 211, 235
NP_811091.1 BT_2178 None 156, 472
NP_811096.1 BT_2183 None 156, 194
NP_811163.1 BT_2250 None 156, 210
NP_811168.1 BT_2255 None 235, 329
NP_811276.1 BT_2363 None 58, 235
NP_811448.1 BT_2535 None 156, 242
NP_811457.1 BT_2544 None 156, 445
NP_811459.1 BT_2546 None 156, 168
NP_811587.1 BT_2675 None 40, 156
NP_811588.1 BT_2676 None 40, 156
NP_811662.1 BT_2750 None 208, 235
NP_811663.1 BT_2751 None 87, 235
NP_811687.1 BT_2775 None 235, 429
NP_811840.1 BT_2928 None 235, 358
NP_811886.1 BT_2974 None 235, 472
NP_811948.1 BT_3036 None 156, 427
NP_811991.1 BT_3079 None 156, 168
NP_811998.1 BT_3086 None 50, 235
NP_812036.1 BT_3124 None 235, 263
NP_812057.1 BT_3145 None 156, 353
NP_812058.1 BT_3146 None 156, 250
NP_812098.1 BT_3186 None 156, 444
NP_812104.1 BT_3192 None 179, 235
NP_812110.1 BT_3198 None 23, 235
NP_812302.1 BT_3390 None 156, 415
NP_812384.1 BT_3472 None 156, 384
NP_812427.1 BT_3515 None 156, 215
NP_812428.1 BT_3516 None 141, 156
NP_812535.1 BT_3624 None 235, 272
NP_812948.1 BT_4037 None 168, 235
NP_813007.1 BT_4096 None 156, 235
NP_813026.1 BT_4115 None 235, 429
NP_813275.1 BT_4364 None 156, 301
NP_813434.1 BT_4523 None 168, 235
NP_813435.1 BT_4524 None 62, 235
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_813007.1
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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