Organism : Bacteroides thetaiotaomicron VPI-5482 | Module List :
NP_813261.1 mazG

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for NP_813261.1
(Mouseover regulator name to see its description)

Warning: No Regulators were found for NP_813261.1!

Warning: NP_813261.1 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
5924 2.50e-06 aaaAtttgTAttTTtGCa.c
Loader icon
5925 2.60e+01 aTtaccaaaaaAgaACaaaaAatg
Loader icon
6064 1.80e-09 TAttTTTGC
Loader icon
6065 1.80e+02 gAaAAAaTt.cTAtaTTTgt
Loader icon
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_813261.1

Warning: No Functional annotations were found!

Module neighborhood information for NP_813261.1

NP_813261.1 has total of 46 gene neighbors in modules 100, 170
Gene neighbors (46)
Gene Common Name Description Module membership
NP_809078.1 BT_0165 None 170, 225
NP_809163.1 BT_0250 None 100, 361
NP_809247.1 BT_0334 None 38, 170
NP_809323.1 BT_0410 None 170, 370
NP_809324.1 BT_0411 None 100, 113
NP_809536.1 BT_0623 None 170, 306
NP_809663.1 BT_0750 None 100, 432
NP_809740.1 BT_0827 None 100, 170
NP_809928.1 BT_1015 None 170, 314
NP_810152.1 BT_1239 None 100, 113
NP_810230.1 BT_1317 None 170, 189
NP_810410.1 BT_1497 None 170, 314
NP_810474.1 BT_1561 None 170, 177
NP_810578.1 BT_1665 None 170, 404
NP_810756.1 BT_1843 None 100, 242
NP_811120.1 BT_2207 None 38, 170
NP_811142.1 BT_2229 None 170, 177
NP_811183.1 BT_2270 None 100, 113
NP_811187.1 BT_2274 None 100, 113
NP_811434.1 BT_2521 None 100, 298
NP_811441.1 BT_2528 None 100, 239
NP_811890.1 BT_2978 None 170, 314
NP_812096.1 BT_3184 None 100, 127
NP_812315.1 nusA None 54, 100
NP_812316.1 infB None 54, 100
NP_812559.1 BT_3648 None 100, 127
NP_812560.1 BT_3649 None 100, 412
NP_812633.1 BT_3722 None 127, 170
NP_812634.1 BT_3723 None 170, 309
NP_812635.1 BT_3724 None 170, 370
NP_812642.1 pyrE None 170, 306
NP_812755.1 BT_3844 None 100, 194
NP_812756.1 BT_3845 None 100, 276
NP_812828.1 ppnK None 41, 100
NP_812830.1 BT_3919 None 41, 100
NP_812832.1 BT_3921 None 41, 100
NP_812833.1 BT_3922 None 41, 100
NP_812861.1 BT_3950 None 100, 309
NP_813166.1 BT_4255 None 100, 170
NP_813261.1 mazG None 100, 170
NP_813427.1 BT_4516 None 170, 431
NP_813440.1 BT_4529 None 170, 404
NP_813503.1 BT_4592 None 38, 170
NP_813525.1 BT_4614 None 170, 306
NP_813664.1 BT_4753 None 38, 170
NP_813665.1 BT_4754 None 170, 431
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_813261.1
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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