Organism : Bacillus cereus ATCC14579 | Module List :
BC3706

Transcriptional regulator, MerR family (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3706
(Mouseover regulator name to see its description)

BC3706 is regulated by 26 influences and regulates 27 modules.
Regulators for BC3706 (26)
Regulator Module Operator
BC0122 133 tf
BC0595 133 tf
BC0993 133 tf
BC1841 133 tf
BC2218 133 tf
BC2770 133 tf
BC3706 133 tf
BC3826 133 tf
BC3868 133 tf
BC3922 133 tf
BC4072 133 tf
BC5265 133 tf
BC5332 133 tf
BC0116 142 tf
BC3706 142 tf
BC3814 142 tf
BC3891 142 tf
BC3922 142 tf
BC4170 142 tf
BC4206 142 tf
BC4212 142 tf
BC4499 142 tf
BC5205 142 tf
BC5265 142 tf
BC5332 142 tf
BC5339 142 tf

Warning: BC3706 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
4182 1.90e+02 atAgAtagaAGGag
Loader icon
4183 1.20e+04 GGgGAA
Loader icon
4200 2.60e+02 CCTCCc
Loader icon
4201 2.20e+03 AAaAAgAaAta.gc
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 BC3706

BC3706 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC3706

BC3706 has total of 28 gene neighbors in modules 133, 142
Gene neighbors (28)
Gene Common Name Description Module membership
BC0232 BC0232 hypothetical Membrane Spanning Protein (NCBI ptt file) 142, 300
BC0481 BC0481 Glutaminase (NCBI ptt file) 27, 133
BC1432 BC1432 Proton/sodium-glutamate symport protein (NCBI ptt file) 133, 337
BC1548 BC1548 Endonuclease III (NCBI ptt file) 142, 269
BC1549 BC1549 hypothetical protein (NCBI ptt file) 142, 269
BC1793 BC1793 Chlorohydrolase/deaminase family protein (NCBI ptt file) 92, 133
BC2021 BC2021 High-affinity zinc uptake system protein znuA precursor (NCBI ptt file) 92, 133
BC3604 BC3604 hypothetical Membrane Spanning Protein (NCBI ptt file) 142, 396
BC3705 BC3705 None 133, 142
BC3706 BC3706 Transcriptional regulator, MerR family (NCBI ptt file) 133, 142
BC3765 BC3765 Phosphoglycerol transferase (NCBI ptt file) 133, 382
BC3871 BC3871 Protein yicC (NCBI ptt file) 142, 275
BC3892 BC3892 Ribosomal large subunit pseudouridine synthase D (NCBI ptt file) 133, 192
BC3922 BC3922 Prespore specific transcriptional activator rsfA (NCBI ptt file) 92, 142
BC4285 BC4285 None 27, 133
BC4507 BC4507 Aquaporin (NCBI ptt file) 92, 133
BC4795 BC4795 hypothetical Membrane Spanning Protein (NCBI ptt file) 133, 221
BC4911 BC4911 Arsenical pump membrane protein (NCBI ptt file) 133, 236
BC5012 BC5012 Chloramphenicol resistance protein (NCBI ptt file) 92, 133
BC5205 BC5205 Transcriptional regulatory protein levR (NCBI ptt file) 142, 304
BC5235 BC5235 Nucleoside permease nupC (NCBI ptt file) 92, 133
BC5265 BC5265 Transcriptional regulator, LytR family (NCBI ptt file) 133, 396
BC5314 BC5314 hypothetical protein (NCBI ptt file) 133, 182
BC5330 BC5330 Thymidine kinase (NCBI ptt file) 133, 142
BC5389 BC5389 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 133, 204
BC5449 BC5449 Conserved membrane protein (hemolysin III homolog) (NCBI ptt file) 88, 142
BC5487 BC5487 Jag protein (NCBI ptt file) 142, 396
BC5489 BC5489 Ribonuclease P protein component (NCBI ptt file) 142, 161
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 BC3706
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