Organism : Bacillus cereus ATCC14579 | Module List :
BC3119

D-alanyl-D-alanine carboxypeptidase (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Beta-lactamase class C and other penicillin binding proteins cog/ cog
beta-lactamase activity go/ molecular_function
beta-lactam antibiotic catabolic process go/ biological_process
response to antibiotic go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3119
(Mouseover regulator name to see its description)

BC3119 is regulated by 28 influences and regulates 0 modules.
Regulators for BC3119 (28)
Regulator Module Operator
BC0057 189 tf
BC1080 189 tf
BC1115 189 tf
BC2178 189 tf
BC2469 189 tf
BC2517 189 tf
BC2631 189 tf
BC2672 189 tf
BC2811 189 tf
BC3588 189 tf
BC4104 189 tf
BC4316 189 tf
BC4393 189 tf
BC4930 189 tf
BC0057 155 tf
BC0586 155 tf
BC1059 155 tf
BC1115 155 tf
BC1329 155 tf
BC1335 155 tf
BC1477 155 tf
BC1489 155 tf
BC3332 155 tf
BC3904 155 tf
BC4832 155 tf
BC5175 155 tf
BC5251 155 tf
BC5463 155 tf

Warning: BC3119 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
4226 5.00e-01 attt.gaagAaGgAgAgcg
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4227 8.50e+03 GCccGGcACtG
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4294 7.90e+03 GACcGGC
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4295 2.90e+00 aaaggGGatGagt
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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 BC3119

BC3119 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Beta-lactamase class C and other penicillin binding proteins cog/ cog
beta-lactamase activity go/ molecular_function
beta-lactam antibiotic catabolic process go/ biological_process
response to antibiotic go/ biological_process
Module neighborhood information for BC3119

BC3119 has total of 30 gene neighbors in modules 155, 189
Gene neighbors (30)
Gene Common Name Description Module membership
BC0404 BC0404 Methyl-accepting chemotaxis protein (NCBI ptt file) 102, 155
BC0407 BC0407 Ornithine carbamoyltransferase (NCBI ptt file) 189, 464
BC0561 BC0561 Two-component response regulator (NCBI ptt file) 189, 472
BC0605 BC0605 hypothetical protein (NCBI ptt file) 155, 489
BC0633 BC0633 Spore germination protein KC (NCBI ptt file) 189, 446
BC1278 BC1278 Signal peptidase I (NCBI ptt file) 155, 489
BC1279 BC1279 Spore coat-associated protein N (NCBI ptt file) 155, 185
BC1508 BC1508 hypothetical protein (NCBI ptt file) 123, 155
BC1640 BC1640 hypothetical protein (NCBI ptt file) 155, 248
BC2317 BC2317 Na(+)-linked D-alanine glycine permease (NCBI ptt file) 125, 155
BC2347 BC2347 Acetyltransferase (NCBI ptt file) 189, 522
BC2451 BC2451 Peptide synthetase (NCBI ptt file) 4, 155
BC2467 BC2467 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 189, 238
BC2631 BC2631 Transcriptional regulator, ArsR family (NCBI ptt file) 189, 358
BC2694 BC2694 hypothetical protein (NCBI ptt file) 128, 189
BC2728 BC2728 hypothetical Cytosolic Protein (NCBI ptt file) 189, 358
BC2945 BC2945 hypothetical protein (NCBI ptt file) 189, 224
BC3076 BC3076 Acetyltransferase (NCBI ptt file) 189, 340
BC3119 BC3119 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 155, 189
BC3363 BC3363 hypothetical protein (NCBI ptt file) 23, 189
BC3485 BC3485 Agmatine deiminase (NCBI ptt file) 155, 502
BC3500 BC3500 hypothetical protein (NCBI ptt file) 97, 155
BC3502 BC3502 IG hypothetical 17676 (NCBI ptt file) 189, 520
BC4041 BC4041 hypothetical protein (NCBI ptt file) 155, 264
BC4533 BC4533 Bacitracin transport permease protein BCRB (NCBI ptt file) 155, 239
BC4695 BC4695 Metal-dependent hydrolase (NCBI ptt file) 23, 189
BC4697 BC4697 hypothetical protein (NCBI ptt file) 78, 155
BC4832 BC4832 Transcriptional regulator, AraC family (NCBI ptt file) 155, 234
BC4907 BC4907 Superoxide dismutase [Cu-Zn] (NCBI ptt file) 155, 180
BC5257 BC5257 hypothetical protein (NCBI ptt file) 155, 369
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 BC3119
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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