Organism : Bacillus cereus ATCC14579 | Module List :
BC2471

Penicillin-binding protein transpeptidase (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Cell division protein FtsI/penicillin-binding protein 2 cog/ cog
penicillin binding go/ molecular_function
peptidoglycan-based cell wall biogenesis go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2471
(Mouseover regulator name to see its description)

BC2471 is regulated by 33 influences and regulates 0 modules.
Regulators for BC2471 (33)
Regulator Module Operator
BC0099 499 tf
BC0116 499 tf
BC0607 499 tf
BC0657 499 tf
BC0856 499 tf
BC1337 499 tf
BC1363 499 tf
BC1889 499 tf
BC2770 499 tf
BC3706 499 tf
BC3826 499 tf
BC3868 499 tf
BC3982 499 tf
BC4057 499 tf
BC4499 499 tf
BC0116 388 tf
BC0607 388 tf
BC0657 388 tf
BC1296 388 tf
BC1841 388 tf
BC1889 388 tf
BC2410 388 tf
BC2672 388 tf
BC2770 388 tf
BC3400 388 tf
BC3706 388 tf
BC3814 388 tf
BC3826 388 tf
BC3891 388 tf
BC3982 388 tf
BC4057 388 tf
BC4289 388 tf
BC5332 388 tf

Warning: BC2471 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
4686 3.70e+00 AtaGGaggGGA
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4687 8.80e+02 A.g.a.aAAA.agAAAaaggcAT
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4908 2.80e+03 TtTGGAGG
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4909 4.20e+04 GAAGGGaG
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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 BC2471

BC2471 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Cell division protein FtsI/penicillin-binding protein 2 cog/ cog
penicillin binding go/ molecular_function
peptidoglycan-based cell wall biogenesis go/ biological_process
Module neighborhood information for BC2471

BC2471 has total of 36 gene neighbors in modules 388, 499
Gene neighbors (36)
Gene Common Name Description Module membership
BC0041 BC0041 Corrin/porphyrin methyltransferase (NCBI ptt file) 139, 388
BC0219 BC0219 Glucose uptake protein homolog (NCBI ptt file) 27, 499
BC0803 BC0803 Sodium-dependent phosphate transporter (NCBI ptt file) 257, 388
BC0889 BC0889 Coproporphyrinogen oxidase, anaerobic (NCBI ptt file) 499, 510
BC0895 BC0895 putative pyruvyl-transferase (NCBI ptt file) 499, 510
BC1160 BC1160 S1 RNA binding domain (NCBI ptt file) 499, 510
BC1289 BC1289 Spermidine/putrescine-binding protein (NCBI ptt file) 388, 458
BC1832 BC1832 DNA topoisomerase I (NCBI ptt file) 176, 499
BC1841 BC1841 Transcriptional regulators, LysR family (NCBI ptt file) 75, 388
BC2369 BC2369 Acetyltransferase (NCBI ptt file) 191, 499
BC2370 BC2370 hypothetical protein (NCBI ptt file) 191, 499
BC2391 BC2391 hypothetical protein (NCBI ptt file) 388, 432
BC2471 BC2471 Penicillin-binding protein transpeptidase (NCBI ptt file) 388, 499
BC2505 BC2505 hypothetical protein (NCBI ptt file) 176, 388
BC3183 BC3183 hypothetical Membrane Spanning Protein (NCBI ptt file) 27, 499
BC3307 BC3307 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 176, 388
BC3308 BC3308 Capsule biosynthesis protein capA (NCBI ptt file) 176, 499
BC3644 BC3644 Sodium/proline symporter (NCBI ptt file) 161, 388
BC3665 BC3665 Bacitracin transport permease protein BCRB (NCBI ptt file) 100, 388
BC3666 BC3666 Bacitracin transport ATP-binding protein bcrA (NCBI ptt file) 176, 388
BC3709 BC3709 hypothetical Membrane Spanning Protein (NCBI ptt file) 304, 388
BC3963 BC3963 Transglutaminase (NCBI ptt file) 145, 388
BC4004 BC4004 Competence protein J (NCBI ptt file) 176, 499
BC4005 BC4005 DNA-entry nuclease (NCBI ptt file) 176, 499
BC4135 BC4135 L-serine dehydratase (NCBI ptt file) 176, 388
BC4136 BC4136 L-serine dehydratase (NCBI ptt file) 176, 388
BC4137 BC4137 hypothetical protein (NCBI ptt file) 176, 388
BC4208 BC4208 hypothetical protein (NCBI ptt file) 176, 499
BC4396 BC4396 Molybdopterin biosynthesis MoeB protein (NCBI ptt file) 346, 388
BC5276 BC5276 Phosphotyrosine-protein phosphatase (capsular polysaccharide biosynthesis) (NCBI ptt file) 176, 499
BC5277 BC5277 Tyrosine-protein kinase (capsular polysaccharide biosynthesis) (NCBI ptt file) 176, 499
BC5278 BC5278 Chain length regulator (capsular polysaccharide biosynthesis) (NCBI ptt file) 176, 499
BC5281 BC5281 rod shape-determining protein Mbl (RefSeq) 147, 499
BC5288 BC5288 UDP-N-acetylglucosamine 1-carboxyvinyltransferase (NCBI ptt file) 499, 510
BC5421 BC5421 hypothetical protein (NCBI ptt file) 176, 499
BC5422 BC5422 hypothetical protein (NCBI ptt file) 499, 510
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 BC2471
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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