Organism : Bacillus cereus ATCC14579 | Module List :
BC3356

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 BC3356
(Mouseover regulator name to see its description)

BC3356 is regulated by 31 influences and regulates 13 modules.
Regulators for BC3356 (31)
Regulator Module Operator
BC0051 88 tf
BC0854 88 tf
BC1819 88 tf
BC3313 88 tf
BC3356 88 tf
BC3405 88 tf
BC3706 88 tf
BC3891 88 tf
BC3922 88 tf
BC4316 88 tf
BC4499 88 tf
BC5205 88 tf
BC5256 88 tf
BC5332 88 tf
BC0114 346 tf
BC0607 346 tf
BC0854 346 tf
BC1080 346 tf
BC1703 346 tf
BC1841 346 tf
BC2133 346 tf
BC2514 346 tf
BC3356 346 tf
BC3706 346 tf
BC3868 346 tf
BC3891 346 tf
BC3982 346 tf
BC4499 346 tf
BC4508 346 tf
BC5332 346 tf
BC5361 346 tf

Warning: BC3356 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
4092 9.40e+01 TtAtaAtAgaagggg
Loader icon
4093 1.20e+04 GAGGCC
Loader icon
4604 1.70e-02 AagGGgGagGa
Loader icon
4605 5.50e+02 AcCcCc
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 BC3356

BC3356 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 BC3356

BC3356 has total of 30 gene neighbors in modules 88, 346
Gene neighbors (30)
Gene Common Name Description Module membership
BC0002 BC0002 DNA polymerase III, beta chain (NCBI ptt file) 88, 201
BC0024 BC0024 DNA polymerase III subunit gamma/tau (NCBI ptt file) 88, 252
BC0693 BC0693 hypothetical protein (NCBI ptt file) 346, 431
BC1525 BC1525 hypothetical Membrane Spanning Protein (NCBI ptt file) 64, 88
BC1558 BC1558 hypothetical protein (NCBI ptt file) 346, 485
BC1612 BC1612 Na+/H+ antiporter NapA (inosine-dependent germination) (NCBI ptt file) 88, 481
BC1648 BC1648 hypothetical Cytosolic Protein (NCBI ptt file) 88, 221
BC2195 BC2195 1-acyl-sn-glycerol-3-phosphate acyltransferase (NCBI ptt file) 88, 221
BC2689 BC2689 Oxalate/formate antiporter (NCBI ptt file) 18, 88
BC3313 BC3313 Transcriptional regulator, MarR family (NCBI ptt file) 88, 298
BC3354 BC3354 ATP synthase protein I (NCBI ptt file) 88, 346
BC3355 BC3355 Magnesium and cobalt efflux protein corC (NCBI ptt file) 88, 346
BC3356 BC3356 Transcriptional regulator, MerR family (NCBI ptt file) 88, 346
BC3945 BC3945 Protoheme IX farnesyltransferase (NCBI ptt file) 161, 346
BC4153 BC4153 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 88, 337
BC4186 BC4186 Stage III sporulation protein AH (NCBI ptt file) 10, 346
BC4322 BC4322 ComE operon protein 3 (NCBI ptt file) 161, 346
BC4344 BC4344 Acetyltransferase (NCBI ptt file) 221, 346
BC4396 BC4396 Molybdopterin biosynthesis MoeB protein (NCBI ptt file) 346, 388
BC4509 BC4509 Sodium export permease protein (NCBI ptt file) 346, 461
BC4510 BC4510 Sodium export ATP-binding protein (NCBI ptt file) 346, 461
BC4763 BC4763 ATP synthase protein I (NCBI ptt file) 245, 346
BC5040 BC5040 Alkaline phosphatase like protein (NCBI ptt file) 88, 246
BC5041 BC5041 Na+/H+ antiporter NapA (NCBI ptt file) 88, 246
BC5042 BC5042 TrkA C-terminal domain protein (NCBI ptt file) 88, 246
BC5070 BC5070 hypothetical protein (NCBI ptt file) 88, 245
BC5357 BC5357 Collagen adhesion protein (NCBI ptt file) 88, 313
BC5442 BC5442 Transporter, MFS superfamily (NCBI ptt file) 346, 425
BC5449 BC5449 Conserved membrane protein (hemolysin III homolog) (NCBI ptt file) 88, 142
BC5479 BC5479 Mechanosensitive ion channel (NCBI ptt file) 88, 329
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 BC3356
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