Organism : Bacillus cereus ATCC14579 | Module List :
BC4001

Transcriptional repressor PadR (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
Predicted transcriptional regulators cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4001
(Mouseover regulator name to see its description)

BC4001 is regulated by 32 influences and regulates 24 modules.
Regulators for BC4001 (32)
Regulator Module Operator
BC0123 233 tf
BC0586 233 tf
BC0613 233 tf
BC1710 233 tf
BC2166 233 tf
BC2794 233 tf
BC2801 233 tf
BC3405 233 tf
BC3668 233 tf
BC3706 233 tf
BC4001 233 tf
BC4029 233 tf
BC4072 233 tf
BC4670 233 tf
BC5200 233 tf
BC5205 233 tf
BC5332 233 tf
BC0265 1 tf
BC0880 1 tf
BC1680 1 tf
BC1710 1 tf
BC3389 1 tf
BC4001 1 tf
BC4076 1 tf
BC4211 1 tf
BC4670 1 tf
BC4703 1 tf
BC4826 1 tf
BC4902 1 tf
BC5143 1 tf
BC5197 1 tf
BC5481 1 tf

Warning: BC4001 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
3924 2.00e-05 g.aaaa.aggGGaGa
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3925 1.40e+04 GGCaAaGAGCcaCTC
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4382 7.00e-02 gaA.gGagGgg
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4383 1.20e+04 CGTacGGTGC
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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 BC4001

BC4001 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulators cog/ cog
Module neighborhood information for BC4001

BC4001 has total of 41 gene neighbors in modules 1, 233
Gene neighbors (41)
Gene Common Name Description Module membership
BC0290 BC0290 ABC transporter ATP-binding protein uup (NCBI ptt file) 1, 475
BC0626 BC0626 Cardiolipin synthetase (NCBI ptt file) 1, 224
BC0759 BC0759 Serine protease (NCBI ptt file) 233, 507
BC0868 BC0868 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (NCBI ptt file) 233, 507
BC1066 BC1066 Signal transduction protein TRAP (NCBI ptt file) 173, 233
BC1680 BC1680 Transcriptional regulator, XRE family (NCBI ptt file) 1, 337
BC1803 BC1803 Manganese transport protein mntH (NCBI ptt file) 233, 287
BC1806 BC1806 2-dehydropantoate 2-reductase (NCBI ptt file) 107, 233
BC2009 BC2009 hypothetical protein (NCBI ptt file) 1, 438
BC2112 BC2112 None 173, 233
BC2114 BC2114 Glutathione peroxidase (NCBI ptt file) 48, 233
BC3053 BC3053 HesB-like protein (NCBI ptt file) 233, 287
BC3054 BC3054 IG hypothetical 18636 (NCBI ptt file) 233, 287
BC3389 BC3389 Transcriptional regulator, MarR family (NCBI ptt file) 1, 74
BC3478 BC3478 Phosphoglycerate mutase (NCBI ptt file) 233, 491
BC3483 BC3483 N-hydroxyarylamine O-acetyltransferase (NCBI ptt file) 77, 233
BC3548 BC3548 Benzil reductase (NCBI ptt file) 233, 507
BC3599 BC3599 Succinyl-CoA synthetase, alpha subunit-related enzymes (NCBI ptt file) 1, 51
BC3616 BC3616 Aconitate hydratase (NCBI ptt file) 1, 475
BC3743 BC3743 Peptidase T (NCBI ptt file) 77, 233
BC4001 BC4001 Transcriptional repressor PadR (NCBI ptt file) 1, 233
BC4092 BC4092 Stage II sporulation protein M (NCBI ptt file) 233, 511
BC4099 BC4099 hypothetical protein (NCBI ptt file) 233, 286
BC4106 BC4106 Alpha/beta hydrolase (NCBI ptt file) 1, 438
BC4259 BC4259 hypothetical Membrane Spanning Protein (NCBI ptt file) 1, 166
BC4631 BC4631 hypothetical protein (NCBI ptt file) 1, 438
BC4691 BC4691 Thioredoxin (NCBI ptt file) 233, 507
BC4714 BC4714 CarD-like transcriptional regulator (NCBI ptt file) 1, 119
BC4790 BC4790 hypothetical Cytosolic Protein (NCBI ptt file) 1, 438
BC4935 BC4935 HESB protein (NCBI ptt file) 1, 119
BC4952 BC4952 NifU protein (NCBI ptt file) 1, 216
BC4973 BC4973 Lipoic acid synthetase (NCBI ptt file) 1, 118
BC5045 BC5045 hypothetical protein (NCBI ptt file) 1, 284
BC5047 BC5047 IG hypothetical 16995 (NCBI ptt file) 1, 74
BC5048 BC5048 Ferritin (NCBI ptt file) 1, 337
BC5128 BC5128 SsrA-binding protein (NCBI ptt file) 1, 505
BC5142 BC5142 Glutaredoxin (NCBI ptt file) 1, 28
BC5143 BC5143 RNA polymerase sigma-54 factor rpoN (NCBI ptt file) 1, 28
BC5159 BC5159 Thioredoxin reductase (NCBI ptt file) 233, 507
BC5197 BC5197 Transcriptional regulator, MarR family (NCBI ptt file) 1, 119
BC5233 BC5233 D-alanine aminotransferase (NCBI ptt file) 233, 286
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 BC4001
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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