Organism : Bacillus cereus ATCC14579 | Module List :
BC1553

Multimodular transpeptidase-transglycosylase (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
catalytic activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
peptidoglycan-based cell wall go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1553
(Mouseover regulator name to see its description)

BC1553 is regulated by 35 influences and regulates 0 modules.
Regulators for BC1553 (35)
Regulator Module Operator
BC0116 176 tf
BC0473 176 tf
BC0607 176 tf
BC0657 176 tf
BC0954 176 tf
BC1841 176 tf
BC1884 176 tf
BC1889 176 tf
BC2672 176 tf
BC2770 176 tf
BC3706 176 tf
BC3813 176 tf
BC3891 176 tf
BC3982 176 tf
BC4010 176 tf
BC4057 176 tf
BC4204 176 tf
BC4289 176 tf
BC4650 176 tf
BC5339 176 tf
BC0116 192 tf
BC0122 192 tf
BC0607 192 tf
BC0657 192 tf
BC0680 192 tf
BC0856 192 tf
BC1841 192 tf
BC2631 192 tf
BC2672 192 tf
BC2770 192 tf
BC3062 192 tf
BC3814 192 tf
BC3826 192 tf
BC3982 192 tf
BC4010 192 tf

Warning: BC1553 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
4268 2.60e+02 GtTagggGgGG
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4269 4.20e+03 GCTCCGC
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4300 8.00e+01 CGTGcAgtcggc
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4301 4.50e+02 gaGGtGGA
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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 BC1553

BC1553 is enriched for 3 functions in 2 categories.
Enrichment Table (3)
Function System
catalytic activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
peptidoglycan-based cell wall go/ cellular_component
Module neighborhood information for BC1553

BC1553 has total of 36 gene neighbors in modules 176, 192
Gene neighbors (36)
Gene Common Name Description Module membership
BC0504 BC0504 A/G-specific adenine DNA glycosylase (NCBI ptt file) 192, 466
BC0654 BC0654 Sulfate transporter (NCBI ptt file) 192, 312
BC1341 BC1341 Aluminum resistance protein (NCBI ptt file) 192, 476
BC1342 BC1342 6-pyruvoyl tetrahydrobiopterin synthase (NCBI ptt file) 192, 476
BC1343 BC1343 Organic radical activating enzyme (NCBI ptt file) 192, 476
BC1344 BC1344 GTP cyclohydrolase I (NCBI ptt file) 192, 313
BC1527 BC1527 hypothetical protein (NCBI ptt file) 62, 176
BC1553 BC1553 Multimodular transpeptidase-transglycosylase (NCBI ptt file) 176, 192
BC1832 BC1832 DNA topoisomerase I (NCBI ptt file) 176, 499
BC2505 BC2505 hypothetical protein (NCBI ptt file) 176, 388
BC3307 BC3307 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 176, 388
BC3308 BC3308 Capsule biosynthesis protein capA (NCBI ptt file) 176, 499
BC3553 BC3553 Sodium/pantothenate symporter (NCBI ptt file) 192, 312
BC3554 BC3554 Sodium/pantothenate symporter (NCBI ptt file) 177, 192
BC3666 BC3666 Bacitracin transport ATP-binding protein bcrA (NCBI ptt file) 176, 388
BC3708 BC3708 GTP-binding protein hflX (NCBI ptt file) 176, 432
BC3831 BC3831 DNA topoisomerase I (NCBI ptt file) 192, 399
BC3892 BC3892 Ribosomal large subunit pseudouridine synthase D (NCBI ptt file) 133, 192
BC3893 lspA lipoprotein signal peptidase (RefSeq) 139, 192
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
BC4286 BC4286 NIF3-related protein (NCBI ptt file) 161, 192
BC4287 BC4287 hypothetical Cytosolic Protein (NCBI ptt file) 161, 192
BC4444 BC4444 Rod shape-determining protein mreD (NCBI ptt file) 49, 192
BC4445 BC4445 Rod shape-determining protein mreC (NCBI ptt file) 192, 242
BC4446 BC4446 Rod shape-determining protein mreB (NCBI ptt file) 192, 242
BC4462 BC4462 Septum formation protein Maf (NCBI ptt file) 192, 222
BC4696 BC4696 SAM-dependent methyltransferase (NCBI ptt file) 8, 176
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
BC5421 BC5421 hypothetical protein (NCBI ptt file) 176, 499
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 BC1553
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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