Organism : Bacillus cereus ATCC14579 | Module List :
BC2704

Serine protease (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Predicted esterase of the alpha-beta hydrolase superfamily cog/ cog
lipid metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2704
(Mouseover regulator name to see its description)

BC2704 is regulated by 31 influences and regulates 0 modules.
Regulators for BC2704 (31)
Regulator Module Operator
BC0224 460 tf
BC0518 460 tf
BC1296 460 tf
BC1673 460 tf
BC2444 460 tf
BC2904 460 tf
BC3069 460 tf
BC3389 460 tf
BC3493 460 tf
BC3497 460 tf
BC4076 460 tf
BC4211 460 tf
BC4650 460 tf
BC4902 460 tf
BC0116 432 tf
BC0122 432 tf
BC0518 432 tf
BC0598 432 tf
BC0607 432 tf
BC0954 432 tf
BC1337 432 tf
BC2362 432 tf
BC2672 432 tf
BC2770 432 tf
BC3062 432 tf
BC3400 432 tf
BC3826 432 tf
BC3982 432 tf
BC4010 432 tf
BC4057 432 tf
BC4499 432 tf

Warning: BC2704 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
4774 3.80e+00 Aa.aGaGG.at
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4775 8.50e+03 CGGcCcc
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4830 2.70e-03 aGGaGG
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4831 1.60e+01 atGtaAaAAGaAatgGaagg
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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 BC2704

BC2704 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted esterase of the alpha-beta hydrolase superfamily cog/ cog
lipid metabolic process go/ biological_process
Module neighborhood information for BC2704

BC2704 has total of 46 gene neighbors in modules 432, 460
Gene neighbors (46)
Gene Common Name Description Module membership
BC0303 BC0303 Alpha/beta hydrolase (NCBI ptt file) 10, 432
BC0365 BC0365 Nitrogen regulation protein NIFR3 (NCBI ptt file) 399, 432
BC0607 BC0607 Transcriptional regulator, LytR family (NCBI ptt file) 159, 432
BC0902 BC0902 S-layer protein / N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 425, 432
BC1118 BC1118 Two-component sensor kinase yvrG (NCBI ptt file) 230, 460
BC1247 BC1247 hypothetical protein (NCBI ptt file) 92, 432
BC1311 BC1311 Small acid-soluble spore protein (NCBI ptt file) 208, 460
BC1337 BC1337 Transcriptional regulator, MarR family (NCBI ptt file) 432, 479
BC1574 BC1574 IAA acetyltransferase (NCBI ptt file) 223, 460
BC1673 BC1673 Transcriptional regulator (NCBI ptt file) 460, 522
BC1674 BC1674 Branched-chain amino acid transport protein azlC (NCBI ptt file) 460, 522
BC1795 BC1795 hypothetical protein (NCBI ptt file) 460, 524
BC2093 BC2093 hypothetical protein (NCBI ptt file) 208, 460
BC2170 BC2170 Sodium-dependent leucine transporter (NCBI ptt file) 297, 460
BC2171 BC2171 Proline iminopeptidase (NCBI ptt file) 297, 460
BC2185 BC2185 Protein ecsB (NCBI ptt file) 341, 432
BC2330 BC2330 Zn-dependent hydrolase (NCBI ptt file) 453, 460
BC2391 BC2391 hypothetical protein (NCBI ptt file) 388, 432
BC2554 BC2554 hypothetical protein (NCBI ptt file) 257, 432
BC2704 BC2704 Serine protease (NCBI ptt file) 432, 460
BC2710 BC2710 NADPH-dependent glutamate synthase beta chain and related oxidoreductases (NCBI ptt file) 460, 462
BC3027 BC3027 hypothetical protein (NCBI ptt file) 460, 525
BC3068 BC3068 Kinase autophosphorylation inhibitor kipI (NCBI ptt file) 460, 525
BC3069 BC3069 Transcriptional regulator kipR (NCBI ptt file) 460, 525
BC3135 BC3135 Carboxymethylenebutenolidase-related protein (NCBI ptt file) 256, 460
BC3259 BC3259 hypothetical Membrane Spanning Protein (NCBI ptt file) 404, 460
BC3284 BC3284 hypothetical protein (NCBI ptt file) 404, 460
BC3287 BC3287 hypothetical protein (NCBI ptt file) 404, 460
BC3520 BC3520 Methyl-accepting chemotaxis protein (NCBI ptt file) 460, 492
BC3708 BC3708 GTP-binding protein hflX (NCBI ptt file) 176, 432
BC3764 BC3764 NAD(FAD)-utilizing dehydrogenases (NCBI ptt file) 308, 460
BC4010 BC4010 Transcriptional regulator, LacI family (NCBI ptt file) 139, 432
BC4264 BC4264 Phosphoglucomutase (NCBI ptt file) 60, 460
BC4499 BC4499 Transcriptional regulator, TetR family (NCBI ptt file) 75, 432
BC4646 BC4646 Small acid-soluble spore protein (NCBI ptt file) 254, 460
BC4948 BC4948 Internalin G (NCBI ptt file) 230, 460
BC4949 BC4949 hypothetical protein (NCBI ptt file) 230, 460
BC5026 BC5026 hypothetical protein (NCBI ptt file) 67, 432
BC5027 BC5027 Protein erfK/srfK precursor (NCBI ptt file) 67, 432
BC5063 BC5063 UDP-N-acetylenolpyruvoylglucosamine reductase (NCBI ptt file) 37, 432
BC5108 BC5108 Zinc finger protein (NCBI ptt file) 254, 460
BC5274 BC5274 UDP-N-acetylglucosamine 4,6-dehydratase (NCBI ptt file) 460, 492
BC5275 BC5275 UTP--glucose-1-phosphate uridylyltransferase (NCBI ptt file) 460, 492
BC5289 BC5289 hypothetical protein (NCBI ptt file) 319, 432
BC5290 BC5290 hypothetical protein (NCBI ptt file) 319, 432
BC5407 BC5407 Chloride channel protein (NCBI ptt file) 67, 432
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 BC2704
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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