Organism : Bacillus cereus ATCC14579 | Module List :
BC2456

Peptide synthetase (NCBI ptt file)

CircVis
Functional Annotations (10)
Function System
Non-ribosomal peptide synthetase modules and related proteins cog/ cog
rhodopsin-like receptor activity go/ molecular_function
G-protein coupled receptor signaling pathway go/ biological_process
biosynthetic process go/ biological_process
integral to membrane go/ cellular_component
hydrolase activity, acting on ester bonds go/ molecular_function
ligase activity go/ molecular_function
phosphopantetheine binding go/ molecular_function
cofactor binding go/ molecular_function
AA-adenyl-dom tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2456
(Mouseover regulator name to see its description)

BC2456 is regulated by 26 influences and regulates 0 modules.
Regulators for BC2456 (26)
Regulator Module Operator
BC0073 150 tf
BC0213 150 tf
BC0356 150 tf
BC0518 150 tf
BC0613 150 tf
BC0840 150 tf
BC1673 150 tf
BC1884 150 tf
BC2766 150 tf
BC2903 150 tf
BC2904 150 tf
BC4076 150 tf
BC4581 150 tf
BC4661 150 tf
BC4902 150 tf
BC1335 347 tf
BC1439 347 tf
BC1603 347 tf
BC2386 347 tf
BC2469 347 tf
BC2988 347 tf
BC4256 347 tf
BC4652 347 tf
BC4670 347 tf
BC5024 347 tf
BC5481 347 tf

Warning: BC2456 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
4216 7.50e+04 CacGGG
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4217 1.80e+03 tAGtgAgggGaA
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4606 2.40e+01 ActttGggaAgcgGc
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4607 2.30e+01 ataGgAGG
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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 BC2456

BC2456 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Non-ribosomal peptide synthetase modules and related proteins cog/ cog
rhodopsin-like receptor activity go/ molecular_function
G-protein coupled receptor signaling pathway go/ biological_process
biosynthetic process go/ biological_process
integral to membrane go/ cellular_component
hydrolase activity, acting on ester bonds go/ molecular_function
ligase activity go/ molecular_function
phosphopantetheine binding go/ molecular_function
cofactor binding go/ molecular_function
AA-adenyl-dom tigr/ tigrfam
Module neighborhood information for BC2456

BC2456 has total of 50 gene neighbors in modules 150, 347
Gene neighbors (50)
Gene Common Name Description Module membership
BC1020 BC1020 hypothetical Membrane Associated Protein (NCBI ptt file) 9, 150
BC1103 BC1103 hypothetical protein (NCBI ptt file) 52, 150
BC1104 BC1104 hypothetical protein (NCBI ptt file) 150, 522
BC1439 BC1439 Two-component response regulator yvqC (NCBI ptt file) 76, 347
BC1474 BC1474 ResB protein (NCBI ptt file) 150, 357
BC1475 BC1475 ResB protein (NCBI ptt file) 150, 357
BC1476 BC1476 Protein resC (NCBI ptt file) 150, 357
BC1502 BC1502 hypothetical protein (NCBI ptt file) 38, 347
BC1523 BC1523 Menaquinol-cytochrome c reductase cytochrome b subunit (NCBI ptt file) 150, 405
BC1524 BC1524 Menaquinol-cytochrome c reductase cytochrome c subunit (NCBI ptt file) 48, 150
BC2271 BC2271 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 244, 347
BC2396 BC2396 hypothetical protein (NCBI ptt file) 347, 526
BC2413 BC2413 Phage protein (NCBI ptt file) 150, 154
BC2414 BC2414 Phage protein (NCBI ptt file) 150, 407
BC2446 BC2446 hypothetical Membrane Spanning Protein (NCBI ptt file) 150, 157
BC2455 BC2455 Peptide synthetase (NCBI ptt file) 347, 484
BC2456 BC2456 Peptide synthetase (NCBI ptt file) 150, 347
BC2457 BC2457 4'-phosphopantetheinyl transferase (NCBI ptt file) 162, 347
BC2625 BC2625 DNA integration/recombination/invertion protein (NCBI ptt file) 150, 485
BC2626 BC2626 DNA integration/recombination/invertion protein (NCBI ptt file) 150, 485
BC2627 BC2627 hypothetical protein (NCBI ptt file) 150, 204
BC2628 BC2628 hypothetical protein (NCBI ptt file) 150, 204
BC2644 BC2644 hypothetical protein (NCBI ptt file) 150, 509
BC2784 BC2784 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 150, 358
BC2785 BC2785 hypothetical protein (NCBI ptt file) 24, 150
BC2867 BC2867 Alpha/beta hydrolase (NCBI ptt file) 150, 253
BC2952 BC2952 enterotoxin / cell-wall binding protein (NCBI ptt file) 96, 150
BC3004 BC3004 Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file) 347, 484
BC3111 BC3111 Spore germination protein BB (NCBI ptt file) 347, 384
BC3162 BC3162 Bicyclomycin resistance protein (NCBI ptt file) 150, 218
BC3164 BC3164 Xanthine dehydrogenase (molybdopterin-guanine dinucleotide biosynthesis subunit) (NCBI ptt file) 347, 407
BC3165 BC3165 Xanthine dehydrogenase subunit (NCBI ptt file) 347, 407
BC3167 BC3167 Xanthine dehydrogenase FAD-binding subunit (NCBI ptt file) 3, 347
BC3168 BC3168 Xanthine dehydrogenase molybdopterin-binding subunit (NCBI ptt file) 3, 347
BC3217 BC3217 putative phosphohydrolases, Icc family (NCBI ptt file) 202, 347
BC3233 BC3233 Glucose/mannose transporter (NCBI ptt file) 347, 407
BC3235 BC3235 Glucose/mannose transporter (NCBI ptt file) 130, 347
BC3249 BC3249 Phosphoserine aminotransferase (NCBI ptt file) 150, 359
BC3256 BC3256 Phage protein (NCBI ptt file) 347, 519
BC3285 BC3285 hypothetical protein (NCBI ptt file) 150, 254
BC3496 BC3496 None 223, 347
BC3857 BC3857 Thiamin pyrophosphokinase (NCBI ptt file) 347, 407
BC4114 BC4114 Biotin synthase (NCBI ptt file) 150, 202
BC4192 BC4192 Stage III sporulation protein AB (NCBI ptt file) 162, 347
BC4217 BC4217 ABC transporter permease protein (NCBI ptt file) 52, 150
BC4218 BC4218 ABC transporter permease protein (NCBI ptt file) 52, 150
BC4219 BC4219 ABC transporter permease protein (NCBI ptt file) 150, 341
BC4221 BC4221 ABC transporter ATP-binding protein (NCBI ptt file) 83, 150
BC4715 BC4715 Glucose 1-dehydrogenase (NCBI ptt file) 150, 256
BC5079 BC5079 Short chain dehydrogenase (NCBI ptt file) 83, 150
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 BC2456
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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