Organism : Bacillus cereus ATCC14579 | Module List :
BC0452

Ribonuclease BN (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Predicted membrane protein cog/ cog
ribonuclease activity go/ molecular_function
yihY_not_rbn tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0452
(Mouseover regulator name to see its description)

BC0452 is regulated by 17 influences and regulates 0 modules.
Regulators for BC0452 (17)
Regulator Module Operator
BC1695 303 tf
BC2410 303 tf
BC2672 303 tf
BC2738 303 tf
BC3332 303 tf
BC3813 303 tf
BC3982 303 tf
BC4072 303 tf
BC0647 253 tf
BC2903 253 tf
BC3332 253 tf
BC3476 253 tf
BC4204 253 tf
BC4222 253 tf
BC4336 253 tf
BC5197 253 tf
BC5205 253 tf

Warning: BC0452 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
4422 4.70e+03 GGtGGcC
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4423 2.20e+03 aAAggtgtcGaA
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4520 3.60e+00 AaAGcaGGcGa
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4521 4.40e+01 GAGCTTGTGCTCGCCTTTCATTCC
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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 BC0452

BC0452 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Predicted membrane protein cog/ cog
ribonuclease activity go/ molecular_function
yihY_not_rbn tigr/ tigrfam
Module neighborhood information for BC0452

BC0452 has total of 29 gene neighbors in modules 253, 303
Gene neighbors (29)
Gene Common Name Description Module membership
BC0452 BC0452 Ribonuclease BN (NCBI ptt file) 253, 303
BC0538 BC0538 hypothetical protein (NCBI ptt file) 303, 333
BC1693 BC1693 putative hydrolase (NCBI ptt file) 227, 303
BC1788 BC1788 Lysophospholipase L2 (NCBI ptt file) 209, 253
BC1833 BC1833 hypothetical protein (NCBI ptt file) 52, 253
BC2043 BC2043 IG hypothetical 17883 (NCBI ptt file) 303, 504
BC2222 BC2222 Oligopeptide transport system permease protein oppB (NCBI ptt file) 253, 339
BC2276 BC2276 Spore germination protein PF (NCBI ptt file) 31, 303
BC2412 BC2412 ABC transporter permease protein (NCBI ptt file) 163, 253
BC2629 BC2629 Methionyl-tRNA formyltransferase (NCBI ptt file) 209, 253
BC2751 BC2751 IG hypothetical 17041 (NCBI ptt file) 253, 459
BC2813 BC2813 CAAX amino terminal protease family (NCBI ptt file) 253, 487
BC2867 BC2867 Alpha/beta hydrolase (NCBI ptt file) 150, 253
BC2928 BC2928 hydrolase (NCBI ptt file) 253, 307
BC3066 BC3066 Lactam utilization protein LAMB (NCBI ptt file) 303, 358
BC3171 BC3171 Methyltransferase (NCBI ptt file) 108, 253
BC3215 BC3215 hypothetical protein (NCBI ptt file) 30, 253
BC3445 BC3445 hypothetical protein (NCBI ptt file) 303, 415
BC3656 BC3656 Methyltransferase (NCBI ptt file) 218, 303
BC3752 BC3752 None 128, 303
BC4015 BC4015 Oligo-1,6-glucosidase (NCBI ptt file) 294, 303
BC4350 BC4350 hypothetical Exported Protein (NCBI ptt file) 52, 253
BC4353 BC4353 Pterin-4-alpha-carbinolamine dehydratase (NCBI ptt file) 158, 303
BC4667 BC4667 Ankyrin (NCBI ptt file) 303, 317
BC4933 BC4933 Methyltransferase (NCBI ptt file) 303, 440
BC4954 BC4954 CotS-related protein (NCBI ptt file) 220, 303
BC4955 BC4955 Low temperature requirement C protein (NCBI ptt file) 281, 303
BC5208 BC5208 cellobiose phosphotransferase system celC (NCBI ptt file) 220, 303
BC5359 BC5359 Aminopeptidase Y (NCBI ptt file) 220, 303
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 BC0452
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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