Organism : Bacillus cereus ATCC14579 | Module List :
BC1047

Protease production regulatory protein hpr (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1047
(Mouseover regulator name to see its description)

BC1047 is regulated by 20 influences and regulates 10 modules.
Regulators for BC1047 (20)
Regulator Module Operator
BC0410 199 tf
BC1047 199 tf
BC2766 199 tf
BC3224 199 tf
BC3244 199 tf
BC3332 199 tf
BC3653 199 tf
BC4570 199 tf
BC4960 199 tf
BC0518 30 tf
BC1253 30 tf
BC2362 30 tf
BC2526 30 tf
BC2904 30 tf
BC3449 30 tf
BC3700 30 tf
BC4211 30 tf
BC4314 30 tf
BC4661 30 tf
BC4960 30 tf

Warning: BC1047 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
3982 3.40e+02 AA.GgaGgaGaGtg
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3983 2.50e+04 GGTcCcCaTCG
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4314 1.50e-08 atGaAAGCGtt
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4315 7.80e-05 aAGGaGGagtt
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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 BC1047

BC1047 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC1047

BC1047 has total of 67 gene neighbors in modules 30, 199
Gene neighbors (67)
Gene Common Name Description Module membership
BC0373 BC0373 Na+/H+ antiporter NnaC (NCBI ptt file) 197, 199
BC0399 BC0399 Oxidoreductase (NCBI ptt file) 30, 85
BC0620 BC0620 Ubiquinone/menaquinone biosynthesis methyltransferase UBIE (NCBI ptt file) 199, 248
BC0643 BC0643 Arginine permease (NCBI ptt file) 199, 473
BC0809 BC0809 PTS system, diacetylchitobiose-specific IIC component (NCBI ptt file) 199, 387
BC0900 BC0900 hypothetical protein (NCBI ptt file) 199, 225
BC0979 BC0979 Dihydroxyacetone kinase (NCBI ptt file) 72, 199
BC0981 BC0981 Dihydroxyacetone kinase (NCBI ptt file) 199, 220
BC1034 BC1034 Glycerol uptake facilitator protein (NCBI ptt file) 199, 516
BC1047 BC1047 Protease production regulatory protein hpr (NCBI ptt file) 30, 199
BC1065 BC1065 hypothetical Membrane Spanning Protein (NCBI ptt file) 30, 453
BC1185 BC1185 Oligopeptide-binding protein oppA (NCBI ptt file) 199, 387
BC1333 BC1333 CBS domain containing protein (NCBI ptt file) 100, 199
BC1389 BC1389 Proton/sodium-glutamate symport protein (NCBI ptt file) 199, 264
BC1596 BC1596 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 199, 381
BC1625 BC1625 Chemotaxis motA protein (NCBI ptt file) 30, 199
BC1626 BC1626 Chemotaxis motB protein (NCBI ptt file) 30, 199
BC1656 BC1656 Flagellin (NCBI ptt file) 30, 85
BC1708 BC1708 hypothetical protein (NCBI ptt file) 30, 130
BC1723 BC1723 Prolipoprotein diacylglyceryl transferase (NCBI ptt file) 30, 250
BC1758 BC1758 hypothetical Membrane Spanning Protein (NCBI ptt file) 30, 147
BC1823 BC1823 Cytidine deaminase (NCBI ptt file) 199, 250
BC2080 BC2080 hypothetical Membrane Associated Protein (NCBI ptt file) 30, 502
BC2081 BC2081 DNA segregation ATPase and related proteins (FtsK/SpoIIIE family) (NCBI ptt file) 30, 502
BC2085 BC2085 hypothetical protein (NCBI ptt file) 30, 502
BC2329 BC2329 Zinc uptake transporter (NCBI ptt file) 199, 250
BC2362 BC2362 Transcriptional regulators, LysR family (NCBI ptt file) 30, 85
BC2526 BC2526 Transcriptional regulator, GntR family (NCBI ptt file) 30, 428
BC2617 BC2617 Cysteine dioxygenase (NCBI ptt file) 199, 327
BC2766 BC2766 Sigma-54-dependent transcriptional activator (NCBI ptt file) 199, 415
BC2851 BC2851 hypothetical protein (NCBI ptt file) 199, 516
BC2876 BC2876 Acetyltransferase (NCBI ptt file) 30, 364
BC2901 BC2901 ABC transporter permease protein (NCBI ptt file) 30, 204
BC2904 BC2904 Transcriptional regulator, GntR family (NCBI ptt file) 30, 60
BC2962 BC2962 Sugar transport system permease protein (NCBI ptt file) 199, 334
BC2965 BC2965 Sugar (pentulose and hexulose) kinases (NCBI ptt file) 186, 199
BC3113 BC3113 Two-component response regulator ycbB (NCBI ptt file) 30, 199
BC3180 BC3180 Low temperature requirement protein A (NCBI ptt file) 199, 410
BC3185 BC3185 hypothetical protein (NCBI ptt file) 197, 199
BC3189 BC3189 Serine transporter (NCBI ptt file) 199, 213
BC3214 BC3214 hypothetical protein (NCBI ptt file) 30, 489
BC3215 BC3215 hypothetical protein (NCBI ptt file) 30, 253
BC3224 BC3224 Transcriptional regulator, ArsR family (NCBI ptt file) 199, 264
BC3225 BC3225 Macrolide-efflux protein (NCBI ptt file) 199, 401
BC3261 BC3261 hypothetical protein (NCBI ptt file) 30, 279
BC3452 BC3452 hypothetical protein (NCBI ptt file) 199, 225
BC3495 BC3495 Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) 199, 213
BC3510 BC3510 hypothetical protein (NCBI ptt file) 30, 291
BC3618 BC3618 Peptidoglycan N-acetylglucosamine deacetylase (NCBI ptt file) 30, 517
BC3631 BC3631 Medium-chain-fatty-acid--CoA ligase (NCBI ptt file) 199, 213
BC3694 BC3694 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 30, 279
BC3695 BC3695 holin (NCBI ptt file) 30, 279
BC3698 BC3698 Cell wall endopeptidase, family M23/M37 (NCBI ptt file) 30, 279
BC3699 BC3699 Antigen (NCBI ptt file) 30, 279
BC3700 BC3700 Phage protein (NCBI ptt file) 30, 197
BC4241 BC4241 hypothetical protein (NCBI ptt file) 7, 199
BC4512 BC4512 Chemotaxis motB protein (NCBI ptt file) 30, 158
BC4591 BC4591 MaoC family protein (NCBI ptt file) 199, 334
BC4619 BC4619 hypothetical protein (NCBI ptt file) 30, 316
BC4661 BC4661 Acetoin utilization acuB protein (NCBI ptt file) 30, 516
BC4780 BC4780 ABC transporter permease protein (NCBI ptt file) 141, 199
BC4784 BC4784 hypothetical protein (NCBI ptt file) 199, 504
BC4960 BC4960 Transcriptional regulator, DeoR family (NCBI ptt file) 30, 334
BC5217 BC5217 PTS system, lichenan oligosaccharide-specific IIB component (NCBI ptt file) 199, 339
BC5320 BC5320 PTS system, glucose-specific IIA component (NCBI ptt file) 74, 199
BC5438 BC5438 Murein hydrolase export regulator (NCBI ptt file) 199, 434
BC5439 BC5439 Murein hydrolase exporter (NCBI ptt file) 197, 199
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 BC1047
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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