Organism : Bacillus cereus ATCC14579 | Module List :
BC4165

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

CircVis
Functional Annotations (10)
Function System
Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains cog/ cog
two-component sensor activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
sensory_box tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4165
(Mouseover regulator name to see its description)

BC4165 is regulated by 16 influences and regulates 4 modules.
Regulators for BC4165 (16)
Regulator Module Operator
BC0073 518 tf
BC0082 518 tf
BC3690 518 tf
BC0954 277 tf
BC1680 277 tf
BC1710 277 tf
BC1915 277 tf
BC2108 277 tf
BC3244 277 tf
BC3255 277 tf
BC4076 277 tf
BC4165 277 tf
BC4256 277 tf
BC4826 277 tf
BC4930 277 tf
BC5010 277 tf

Warning: BC4165 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
4470 8.70e-01 a.AagGAgcgc
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4471 4.00e+03 GAAaGg
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4946 8.20e+00 cg.TtatAgaggcaaAggGg
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4947 1.30e+01 GgaAAGGAAgG
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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 BC4165

BC4165 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains cog/ cog
two-component sensor activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
sensory_box tigr/ tigrfam
Module neighborhood information for BC4165

BC4165 has total of 46 gene neighbors in modules 277, 518
Gene neighbors (46)
Gene Common Name Description Module membership
BC0028 BC0028 SigmaK-factor processing regulatory protein BofA (NCBI ptt file) 245, 277
BC0074 BC0074 33 kDa chaperonin (NCBI ptt file) 240, 518
BC0076 BC0076 Para-aminobenzoate synthase component I (NCBI ptt file) 493, 518
BC0077 BC0077 Anthranilate synthase component II (NCBI ptt file) 493, 518
BC0078 BC0078 4-amino-4-deoxychorismate lyase (NCBI ptt file) 493, 518
BC0079 BC0079 Dihydropteroate synthase (NCBI ptt file) 493, 518
BC0080 BC0080 Dihydroneopterin aldolase (NCBI ptt file) 493, 518
BC0081 BC0081 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (NCBI ptt file) 493, 518
BC0082 BC0082 Transcriptional regulator, Xre family (NCBI ptt file) 493, 518
BC0083 BC0083 Nif3 family protein (NCBI ptt file) 493, 518
BC0263 BC0263 hypothetical protein (NCBI ptt file) 276, 518
BC0264 BC0264 Alanine racemase (NCBI ptt file) 72, 518
BC0496 BC0496 Dihydroorotase (NCBI ptt file) 277, 281
BC0500 BC0500 hypothetical protein (NCBI ptt file) 277, 509
BC0501 BC0501 IG hypothetical 18102 (NCBI ptt file) 165, 277
BC0683 BC0683 hypothetical protein (NCBI ptt file) 277, 435
BC2373 BC2373 DNA integration/recombination/invertion protein (NCBI ptt file) 140, 277
BC3074 BC3074 None 31, 277
BC3085 BC3085 None 60, 277
BC3315 BC3315 6-aminohexanoate-dimer hydrolase (NCBI ptt file) 108, 277
BC3853 BC3853 ATP-dependent DNA helicase recG (NCBI ptt file) 240, 518
BC3926 BC3926 ATP-dependent protease La (NCBI ptt file) 451, 518
BC3927 BC3927 Serine protease (NCBI ptt file) 451, 518
BC4122 BC4122 None 139, 277
BC4157 BC4157 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (NCBI ptt file) 205, 277
BC4158 BC4158 2-oxoisovalerate dehydrogenase beta subunit (NCBI ptt file) 205, 277
BC4159 BC4159 2-oxoisovalerate dehydrogenase alpha subunit (NCBI ptt file) 205, 277
BC4160 BC4160 Dihydrolipoamide dehydrogenase (NCBI ptt file) 205, 277
BC4161 BC4161 Branched-chain-fatty-acid kinase (NCBI ptt file) 205, 277
BC4162 BC4162 Leucine dehydrogenase (NCBI ptt file) 205, 277
BC4163 BC4163 Phosphate butyryltransferase (NCBI ptt file) 205, 277
BC4165 BC4165 Sigma-54-dependent transcriptional activator (NCBI ptt file) 277, 518
BC4176 BC4176 1-deoxy-D-xylulose 5-phosphate synthase (NCBI ptt file) 451, 518
BC4303 BC4303 putative stage IV sporulation protein (NCBI ptt file) 17, 518
BC4478 BC4478 ATP-dependent protease La (NCBI ptt file) 277, 361
BC4485 BC4485 hypothetical Cytosolic Protein (NCBI ptt file) 59, 518
BC4486 BC4486 hypothetical protein (NCBI ptt file) 59, 518
BC4487 BC4487 Superfamily I DNA and RNA helicases (NCBI ptt file) 518, 524
BC4586 BC4586 Formamidopyrimidine-DNA glycosylase (NCBI ptt file) 164, 518
BC4751 BC4751 Sulfite reductase [NADPH] flavoprotein alpha-component (NCBI ptt file) 245, 277
BC4808 BC4808 Thiamine transporter (NCBI ptt file) 277, 414
BC4901 BC4901 Aromatic amino acid aminotransferase (NCBI ptt file) 484, 518
BC5435 BC5435 Acriflavin resistance plasma membrane protein (NCBI ptt file) 277, 425
BC5469 BC5469 None 493, 518
BC5471 BC5471 LSU ribosomal protein L9P (NCBI ptt file) 493, 518
BC5472 BC5472 phosphoesterase, DHH family protein (NCBI ptt file) 493, 518
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 BC4165
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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