Organism : Bacillus cereus ATCC14579 | Module List :
BC2837

Sigma-54-dependent transcriptional activator (NCBI ptt file)

CircVis
Functional Annotations (9)
Function System
Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
signal transducer activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
signal transduction go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2837
(Mouseover regulator name to see its description)

BC2837 is regulated by 20 influences and regulates 21 modules.
Regulators for BC2837 (20)
Regulator Module Operator
BC0647 168 tf
BC1329 168 tf
BC1818 168 tf
BC2469 168 tf
BC2811 168 tf
BC2837 168 tf
BC3408 168 tf
BC3588 168 tf
BC3903 168 tf
BC5251 168 tf
BC1329 54 tf
BC2401 54 tf
BC2469 54 tf
BC2773 54 tf
BC2837 54 tf
BC2964 54 tf
BC4499 54 tf
BC5024 54 tf
BC5339 54 tf
BC5402 54 tf

Warning: BC2837 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
4028 3.90e-01 Aa.tG.aGGgat
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4029 3.70e+00 tAaaaAaagGcgta
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4252 6.60e+03 GGGcTGc
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4253 1.30e+04 GGAGGAA
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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 BC2837

BC2837 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
signal transducer activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
signal transduction go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
Module neighborhood information for BC2837

BC2837 has total of 30 gene neighbors in modules 54, 168
Gene neighbors (30)
Gene Common Name Description Module membership
BC0619 BC0619 Iron(III) dicitrate transport ATP-binding protein fecE (NCBI ptt file) 54, 446
BC1078 BC1078 Phage infection protein (NCBI ptt file) 54, 339
BC1175 BC1175 hypothetical Cytosolic Protein (NCBI ptt file) 54, 220
BC1347 BC1347 hypothetical protein (NCBI ptt file) 54, 330
BC1469 BC1469 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 54, 355
BC1471 BC1471 Spore maturation protein B (NCBI ptt file) 31, 54
BC2016 BC2016 Amine oxidase [flavin-containing] (NCBI ptt file) 153, 168
BC2613 BC2613 Cytochrome P450 (NCBI ptt file) 54, 196
BC2635 BC2635 Collagen triple helix repeat protein (NCBI ptt file) 46, 54
BC2791 BC2791 Glycine betaine transport ATP-binding protein (NCBI ptt file) 168, 317
BC2800 BC2800 hypothetical Cytosolic Protein (NCBI ptt file) 136, 168
BC2837 BC2837 Sigma-54-dependent transcriptional activator (NCBI ptt file) 54, 168
BC2924 BC2924 Acetyltransferase (NCBI ptt file) 168, 437
BC2953 BC2953 hypothetical protein (NCBI ptt file) 168, 397
BC2963 BC2963 Sugar transport ATP-binding protein (NCBI ptt file) 168, 355
BC3106 BC3106 Small acid-soluble spore protein (NCBI ptt file) 54, 212
BC3108 BC3108 Amino acid permease (NCBI ptt file) 54, 352
BC3466 BC3466 Ferrichrome-binding protein (NCBI ptt file) 54, 419
BC3467 BC3467 Ferrichrome transport system permease protein fhuG (NCBI ptt file) 54, 419
BC3468 BC3468 Ferrichrome transport system permease protein fhuB (NCBI ptt file) 54, 419
BC3583 BC3583 Methyltransferase (NCBI ptt file) 54, 397
BC3630 BC3630 Medium-chain-fatty-acid--CoA ligase (NCBI ptt file) 168, 490
BC3748 BC3748 UDP-N-acetylglucosamine--N-acetylmuramyl-(Pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (NCBI ptt file) 59, 168
BC3875 BC3875 Xaa-Pro dipeptidase (NCBI ptt file) 115, 168
BC4723 BC4723 Molybdopterin biosynthesis MoeB protein (NCBI ptt file) 23, 54
BC4725 BC4725 hypothetical Membrane Spanning Protein (NCBI ptt file) 54, 232
BC4922 BC4922 hypothetical Membrane Associated Protein (NCBI ptt file) 102, 168
BC5209 BC5209 6-phospho-beta-glucosidase (NCBI ptt file) 54, 516
BC5334 BC5334 UDP-N-acetylglucosamine 1-carboxyvinyltransferase (NCBI ptt file) 54, 524
BC5355 BC5355 ABC transporter ATP-binding protein (NCBI ptt file) 54, 469
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 BC2837
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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