Organism : Bacillus cereus ATCC14579 | Module List :
BC1067

Multimodular transpeptidase-transglycosylase PBP 2C (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
Membrane carboxypeptidase (penicillin-binding protein) cog/ cog
peptidase activity go/ molecular_function
penicillin binding go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
peptidoglycan-based cell wall go/ cellular_component
transferase activity, transferring pentosyl groups go/ molecular_function
response to antibiotic go/ biological_process
PBP_1a_fam tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1067
(Mouseover regulator name to see its description)

BC1067 is regulated by 33 influences and regulates 0 modules.
Regulators for BC1067 (33)
Regulator Module Operator
BC2410 424 tf
BC2517 424 tf
BC2549 424 tf
BC2742 424 tf
BC2773 424 tf
BC2904 424 tf
BC2971 424 tf
BC3069 424 tf
BC3449 424 tf
BC3587 424 tf
BC3588 424 tf
BC3792 424 tf
BC4001 424 tf
BC4029 424 tf
BC4256 424 tf
BC4433 424 tf
BC5251 424 tf
BC0116 311 tf
BC0122 311 tf
BC0473 311 tf
BC0613 311 tf
BC1477 311 tf
BC1884 311 tf
BC2109 311 tf
BC2122 311 tf
BC3207 311 tf
BC3792 311 tf
BC3814 311 tf
BC3844 311 tf
BC4603 311 tf
BC4902 311 tf
BC5250 311 tf
BC5481 311 tf

Warning: BC1067 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
4536 6.00e-01 ATagaaaAgGAaggG
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4537 2.90e+03 GGaGGaGGaCTaGC
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4758 3.60e-03 aGGggGc
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4759 2.20e+04 CGCcTTG
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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 BC1067

BC1067 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Membrane carboxypeptidase (penicillin-binding protein) cog/ cog
peptidase activity go/ molecular_function
penicillin binding go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
peptidoglycan-based cell wall go/ cellular_component
transferase activity, transferring pentosyl groups go/ molecular_function
response to antibiotic go/ biological_process
PBP_1a_fam tigr/ tigrfam
Module neighborhood information for BC1067

BC1067 has total of 38 gene neighbors in modules 311, 424
Gene neighbors (38)
Gene Common Name Description Module membership
BC0258 BC0258 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D- alanyl ligase (NCBI ptt file) 283, 311
BC0268 BC0268 Zinc metalloprotease (NCBI ptt file) 212, 424
BC0296 BC0296 GMP synthase [glutamine-hydrolyzing] (NCBI ptt file) 157, 311
BC0326 BC0326 phosphoribosylaminoimidazole-succinocarboxamidesynthase (RefSeq) 424, 524
BC0329 BC0329 Phosphoribosylformylglycinamidine synthase (NCBI ptt file) 424, 524
BC0331 BC0331 Phosphoribosylformylglycinamidine cyclo-ligase (NCBI ptt file) 424, 524
BC0332 BC0332 Phosphoribosylglycinamide formyltransferase (NCBI ptt file) 424, 524
BC0352 BC0352 Glutamyl-tRNA(Gln) amidotransferase subunit B (NCBI ptt file) 145, 311
BC0429 BC0429 Endochitinase (NCBI ptt file) 353, 424
BC1067 BC1067 Multimodular transpeptidase-transglycosylase PBP 2C (NCBI ptt file) 311, 424
BC1068 BC1068 Uroporphyrinogen decarboxylase (NCBI ptt file) 283, 311
BC1069 BC1069 Ferrochelatase (NCBI ptt file) 72, 311
BC1070 BC1070 Protoporphyrinogen oxidase (NCBI ptt file) 311, 382
BC1660 BC1660 Soluble lytic murein transglycosylase (NCBI ptt file) 85, 424
BC1661 BC1661 Flagellar motor switch protein fliN (NCBI ptt file) 311, 424
BC1662 BC1662 Flagellar motor switch protein fliM (NCBI ptt file) 311, 424
BC1663 BC1663 Flagellar motor switch protein fliN (NCBI ptt file) 157, 311
BC1664 BC1664 Flagellar motor switch protein fliN (NCBI ptt file) 157, 311
BC1665 BC1665 Flagellar biosynthetic protein fliP (NCBI ptt file) 157, 311
BC1666 BC1666 Flagellar biosynthetic protein fliQ (NCBI ptt file) 157, 311
BC1667 BC1667 Flagellar biosynthetic protein fliR (NCBI ptt file) 157, 311
BC1668 BC1668 Flagellar biosynthetic protein flhB (NCBI ptt file) 157, 311
BC1985 BC1985 None 139, 311
BC2216 BC2216 Two-component sensor protein yhcY (NCBI ptt file) 279, 424
BC2468 BC2468 Cell elongation specific D,D-transpeptidase (NCBI ptt file) 307, 424
BC2652 BC2652 hypothetical protein (NCBI ptt file) 291, 424
BC3006 BC3006 hypothetical protein (NCBI ptt file) 239, 424
BC3425 BC3425 hypothetical Membrane Associated Protein (NCBI ptt file) 212, 424
BC3696 BC3696 XpaF1 protein (NCBI ptt file) 279, 424
BC3697 BC3697 Phage-related protein (NCBI ptt file) 149, 424
BC3844 BC3844 Signal recognition particle associated protein (NCBI ptt file) 311, 476
BC4029 BC4029 Transcriptional regulator, PadR family (NCBI ptt file) 404, 424
BC4050 BC4050 PTS system, glucose-specific IIABC component (NCBI ptt file) 188, 311
BC4069 BC4069 Stage V sporulation protein AB (NCBI ptt file) 424, 524
BC4662 BC4662 Acetoin utilization acuC protein (NCBI ptt file) 424, 516
BC4738 BC4738 Multidrug resistance protein B (NCBI ptt file) 242, 311
BC5227 BC5227 Thiamine biosynthesis protein thiC (NCBI ptt file) 135, 424
BC5375 BC5375 Multimodular transpeptidase-transglycosylase PBP 2D (NCBI ptt file) 285, 311
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 BC1067
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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