Organism : Bacillus cereus ATCC14579 | Module List :
BC3607

spore peptidoglycan hydrolase (N-acetylglucosaminidase) (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Predicted glycosyl hydrolase cog/ cog
chitinase activity go/ molecular_function
chitin catabolic process go/ biological_process
cell wall macromolecule catabolic process go/ biological_process
cation binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3607
(Mouseover regulator name to see its description)

BC3607 is regulated by 14 influences and regulates 0 modules.
Regulators for BC3607 (14)
Regulator Module Operator
BC0051 430 tf
BC0123 430 tf
BC0158 430 tf
BC1710 430 tf
BC4294 430 tf
BC0122 284 tf
BC0473 284 tf
BC0598 284 tf
BC0958 284 tf
BC3163 284 tf
BC3194 284 tf
BC3653 284 tf
BC3814 284 tf
BC4652 284 tf

Warning: BC3607 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
4484 1.70e-06 CtcCCC
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4485 6.80e+03 TCcCCtaCTT
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4770 2.00e-03 ccTTtCaCctc
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4771 2.30e+02 gCagAccAaGaaaT.GaAA
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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 BC3607

BC3607 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted glycosyl hydrolase cog/ cog
chitinase activity go/ molecular_function
chitin catabolic process go/ biological_process
cell wall macromolecule catabolic process go/ biological_process
cation binding go/ molecular_function
Module neighborhood information for BC3607

BC3607 has total of 52 gene neighbors in modules 284, 430
Gene neighbors (52)
Gene Common Name Description Module membership
BC0129 BC0129 Protein Translation Elongation Factor Tu (EF-TU) (NCBI ptt file) 188, 430
BC0153 BC0153 Methionine aminopeptidase (NCBI ptt file) 292, 430
BC0155 BC0155 LSU ribosomal protein L36P (NCBI ptt file) 292, 430
BC0159 BC0159 LSU ribosomal protein L17P (NCBI ptt file) 90, 430
BC0466 BC0466 Fumarate hydratase (NCBI ptt file) 28, 430
BC0637 BC0637 putative protein kinase (NCBI ptt file) 284, 299
BC0699 BC0699 Arginine permease (NCBI ptt file) 284, 434
BC0958 BC0958 Transcriptional regulator (NCBI ptt file) 284, 316
BC1030 BC1030 hypothetical protein (NCBI ptt file) 228, 430
BC1052 BC1052 Protein ecsC (NCBI ptt file) 216, 284
BC1084 BC1084 hypothetical protein (NCBI ptt file) 128, 284
BC1123 BC1123 Zinc metalloprotease (NCBI ptt file) 13, 284
BC1176 BC1176 hypothetical protein (NCBI ptt file) 263, 284
BC1186 BC1186 hypothetical protein (NCBI ptt file) 52, 284
BC1339 BC1339 hypothetical protein (NCBI ptt file) 216, 284
BC1366 BC1366 SSEB protein (NCBI ptt file) 137, 284
BC1367 BC1367 Muramoyltetrapeptide carboxypeptidase (NCBI ptt file) 46, 284
BC1518 BC1518 Histidinol-phosphate aminotransferase (NCBI ptt file) 284, 302
BC1695 BC1695 Transcriptional regulator, MarR family (NCBI ptt file) 284, 333
BC1958 BC1958 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file) 216, 284
BC1976 BC1976 Membrane protein, MgtC/SapB family (NCBI ptt file) 354, 430
BC1989 BC1989 hypothetical Membrane Spanning Protein (NCBI ptt file) 284, 402
BC2017 BC2017 Ribosomal-protein-serine acetyltransferase (NCBI ptt file) 284, 400
BC2032 BC2032 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 224, 284
BC2152 BC2152 hypothetical protein (NCBI ptt file) 430, 431
BC2186 BC2186 hypothetical protein (NCBI ptt file) 284, 434
BC2209 BC2209 D-amino acid aminotransferase (RefSeq) 120, 284
BC2265 BC2265 hypothetical protein (NCBI ptt file) 284, 299
BC2540 BC2540 hypothetical protein (NCBI ptt file) 285, 430
BC2642 BC2642 None 165, 284
BC2729 BC2729 Penicillin-binding protein (NCBI ptt file) 284, 434
BC2944 BC2944 hypothetical protein (NCBI ptt file) 224, 284
BC2959 BC2959 Malate:quinone oxidoreductase (NCBI ptt file) 264, 284
BC3607 BC3607 spore peptidoglycan hydrolase (N-acetylglucosaminidase) (NCBI ptt file) 284, 430
BC3757 BC3757 hypothetical protein (NCBI ptt file) 430, 475
BC3758 BC3758 Transcriptional regulator, GntR family (NCBI ptt file) 103, 430
BC3794 BC3794 hypothetical protein (NCBI ptt file) 414, 430
BC3795 BC3795 Translocation-enhancing protein tepA (NCBI ptt file) 414, 430
BC4354 BC4354 Glyoxalase family protein (NCBI ptt file) 284, 288
BC4565 BC4565 CAAX amino terminal protease family (NCBI ptt file) 246, 284
BC4671 BC4671 hypothetical protein (NCBI ptt file) 285, 430
BC4908 BC4908 hypothetical Membrane Associated Protein (NCBI ptt file) 20, 284
BC4951 BC4951 hypothetical protein (NCBI ptt file) 98, 284
BC5006 BC5006 Prolyne dehydrogenase (NCBI ptt file) 284, 473
BC5014 BC5014 hypothetical exported repetitive protein (NCBI ptt file) 284, 359
BC5045 BC5045 hypothetical protein (NCBI ptt file) 1, 284
BC5046 BC5046 Lysine decarboxylase family (NCBI ptt file) 20, 284
BC5060 BC5060 hypothetical protein (NCBI ptt file) 385, 430
BC5284 BC5284 ABC transporter permease protein (NCBI ptt file) 123, 284
BC5328 BC5328 Methyltransferase (NCBI ptt file) 285, 430
BC5333 BC5333 Fructose-1,6-bisphosphatase (NCBI ptt file) 224, 284
BC5408 BC5408 2-haloalkanoic acid dehalogenase (NCBI ptt file) 281, 430
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 BC3607
Please add your comments for this gene by using the form below. Your comments will be publicly available.

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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