Organism : Bacillus cereus ATCC14579 | Module List :
BC2833

Dihydrodipicolinate synthase (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
Dihydrodipicolinate synthase/N-acetylneuraminate lyase cog/ cog
dihydrodipicolinate synthase activity go/ molecular_function
diaminopimelate biosynthetic process go/ biological_process
Lysine biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
dapA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2833
(Mouseover regulator name to see its description)

BC2833 is regulated by 34 influences and regulates 0 modules.
Regulators for BC2833 (34)
Regulator Module Operator
BC0356 202 tf
BC0405 202 tf
BC0518 202 tf
BC1131 202 tf
BC1603 202 tf
BC1673 202 tf
BC1756 202 tf
BC1884 202 tf
BC2904 202 tf
BC3207 202 tf
BC3389 202 tf
BC3690 202 tf
BC3693 202 tf
BC3758 202 tf
BC4222 202 tf
BC4256 202 tf
BC4474 202 tf
BC5363 202 tf
BC5481 202 tf
BC0657 484 tf
BC1335 484 tf
BC1818 484 tf
BC1884 484 tf
BC2469 484 tf
BC2517 484 tf
BC2558 484 tf
BC2837 484 tf
BC3224 484 tf
BC3690 484 tf
BC4001 484 tf
BC4170 484 tf
BC4670 484 tf
BC5024 484 tf
BC5402 484 tf

Warning: BC2833 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
4320 2.30e-02 AGGaGg
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4321 3.50e+02 GcAAG.aGaACa
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4878 8.80e-06 CccTtCC.
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4879 3.30e+01 gGGGgAG
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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 BC2833

BC2833 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Dihydrodipicolinate synthase/N-acetylneuraminate lyase cog/ cog
dihydrodipicolinate synthase activity go/ molecular_function
diaminopimelate biosynthetic process go/ biological_process
Lysine biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
dapA tigr/ tigrfam
Module neighborhood information for BC2833

BC2833 has total of 42 gene neighbors in modules 202, 484
Gene neighbors (42)
Gene Common Name Description Module membership
BC0058 BC0058 Transcription-repair coupling factor (NCBI ptt file) 240, 484
BC0113 BC0113 hypothetical Cytosolic Protein (NCBI ptt file) 357, 484
BC0746 BC0746 Regulatory protein TENI (NCBI ptt file) 3, 202
BC0990 BC0990 hypothetical protein (NCBI ptt file) 202, 306
BC1575 BC1575 hypothetical protein (NCBI ptt file) 179, 484
BC1878 BC1878 Phage protein (NCBI ptt file) 202, 469
BC2031 BC2031 Spore coat protein H (NCBI ptt file) 104, 202
BC2086 BC2086 hypothetical protein (NCBI ptt file) 202, 404
BC2159 BC2159 None 202, 282
BC2341 BC2341 None 98, 484
BC2385 BC2385 Dehydrogenase (NCBI ptt file) 202, 393
BC2453 BC2453 Peptide synthetase (NCBI ptt file) 484, 490
BC2454 BC2454 Peptide synthetase (NCBI ptt file) 232, 484
BC2455 BC2455 Peptide synthetase (NCBI ptt file) 347, 484
BC2484 BC2484 Propionyl-CoA carboxylase biotin-containing subunit (NCBI ptt file) 202, 355
BC2832 BC2832 Aldehyde dehydrogenase (NCBI ptt file) 202, 484
BC2833 BC2833 Dihydrodipicolinate synthase (NCBI ptt file) 202, 484
BC3004 BC3004 Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file) 347, 484
BC3031 BC3031 Isoflavone reductase (NCBI ptt file) 484, 512
BC3166 BC3166 Xanthine dehydrogenase iron-sulfur subunit (NCBI ptt file) 407, 484
BC3211 BC3211 NADPH-cytochrome P450 reductase (NCBI ptt file) 484, 506
BC3217 BC3217 putative phosphohydrolases, Icc family (NCBI ptt file) 202, 347
BC3336 BC3336 hypothetical protein (NCBI ptt file) 177, 202
BC3337 BC3337 Acetyltransferase (NCBI ptt file) 202, 223
BC3427 BC3427 Glycosyltransferase (NCBI ptt file) 202, 223
BC3691 BC3691 hypothetical protein (NCBI ptt file) 202, 276
BC3692 BC3692 hypothetical protein (NCBI ptt file) 202, 229
BC4114 BC4114 Biotin synthase (NCBI ptt file) 150, 202
BC4116 BC4116 BioH protein (NCBI ptt file) 135, 202
BC4117 BC4117 8-amino-7-oxononanoate synthase (NCBI ptt file) 135, 202
BC4118 BC4118 Dethiobiotin synthetase (NCBI ptt file) 135, 202
BC4119 BC4119 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI ptt file) 135, 202
BC4318 BC4318 hypothetical protein (NCBI ptt file) 202, 484
BC4319 BC4319 Spore protease (NCBI ptt file) 202, 223
BC4901 BC4901 Aromatic amino acid aminotransferase (NCBI ptt file) 484, 518
BC4930 BC4930 Transcriptional regulator, DeoR family (NCBI ptt file) 202, 464
BC5022 BC5022 Cytolysin immunity CylI (NCBI ptt file) 48, 484
BC5023 BC5023 hypothetical protein (NCBI ptt file) 48, 484
BC5024 BC5024 Transcriptional regulator, PBSX family (NCBI ptt file) 48, 484
BC5202 BC5202 UDP-glucose 6-dehydrogenase (NCBI ptt file) 202, 223
BC5294 BC5294 NADH-quinone oxidoreductase chain K (NCBI ptt file) 321, 484
BC5412 BC5412 Two-component sensor protein yhcY (NCBI ptt file) 202, 223
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 BC2833
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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