Organism : Bacillus cereus ATCC14579 | Module List :
BC2457

4'-phosphopantetheinyl transferase (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Phosphopantetheinyl transferase cog/ cog
magnesium ion binding go/ molecular_function
fatty acid biosynthetic process go/ biological_process
holo-[acyl-carrier-protein] synthase activity go/ molecular_function
macromolecule biosynthetic process go/ biological_process
pantethn_trn tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2457
(Mouseover regulator name to see its description)

BC2457 is regulated by 22 influences and regulates 0 modules.
Regulators for BC2457 (22)
Regulator Module Operator
BC0647 162 tf
BC0648 162 tf
BC1329 162 tf
BC1335 162 tf
BC1439 162 tf
BC1699 162 tf
BC1710 162 tf
BC3903 162 tf
BC3976 162 tf
BC4336 162 tf
BC5282 162 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: BC2457 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
4240 9.60e-03 c.CctcCTctc
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4241 7.60e+02 gggtaTCCCctcaGc
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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 BC2457

BC2457 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Phosphopantetheinyl transferase cog/ cog
magnesium ion binding go/ molecular_function
fatty acid biosynthetic process go/ biological_process
holo-[acyl-carrier-protein] synthase activity go/ molecular_function
macromolecule biosynthetic process go/ biological_process
pantethn_trn tigr/ tigrfam
Module neighborhood information for BC2457

BC2457 has total of 42 gene neighbors in modules 162, 347
Gene neighbors (42)
Gene Common Name Description Module membership
BC0647 BC0647 RNA polymerase ECF-type sigma factor (NCBI ptt file) 25, 162
BC0653 BC0653 hypothetical Cytosolic Protein (NCBI ptt file) 162, 267
BC0784 BC0784 Spore germination protein, gerA family (NCBI ptt file) 131, 162
BC0819 BC0819 Oligopeptide transport system permease protein oppC (NCBI ptt file) 162, 217
BC0838 BC0838 Na+/H+ antiporter NapA (NCBI ptt file) 104, 162
BC1439 BC1439 Two-component response regulator yvqC (NCBI ptt file) 76, 347
BC1502 BC1502 hypothetical protein (NCBI ptt file) 38, 347
BC1737 BC1737 Cardiolipin synthetase (NCBI ptt file) 25, 162
BC2271 BC2271 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 244, 347
BC2344 BC2344 hypothetical protein (NCBI ptt file) 102, 162
BC2396 BC2396 hypothetical protein (NCBI ptt file) 347, 526
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
BC2458 BC2458 Thioesterase (NCBI ptt file) 162, 509
BC2621 BC2621 Signal peptidase I (NCBI ptt file) 158, 162
BC2641 BC2641 hypothetical Cytosolic Protein (NCBI ptt file) 5, 162
BC3004 BC3004 Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file) 347, 484
BC3111 BC3111 Spore germination protein BB (NCBI ptt file) 347, 384
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
BC3256 BC3256 Phage protein (NCBI ptt file) 347, 519
BC3358 BC3358 Glucose-1-phosphate cytidylyltransferase (NCBI ptt file) 162, 181
BC3479 BC3479 Acetyltransferase (NCBI ptt file) 31, 162
BC3480 BC3480 DNA mismatch repair protein mutS (NCBI ptt file) 162, 353
BC3496 BC3496 None 223, 347
BC3516 BC3516 CDP-abequose synthase (NCBI ptt file) 162, 339
BC3517 BC3517 CDP-glucose 4,6-dehydratase (NCBI ptt file) 84, 162
BC3857 BC3857 Thiamin pyrophosphokinase (NCBI ptt file) 347, 407
BC4075 BC4075 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 25, 162
BC4191 BC4191 Stage III sporulation protein AC (NCBI ptt file) 131, 162
BC4192 BC4192 Stage III sporulation protein AB (NCBI ptt file) 162, 347
BC4765 BC4765 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 67, 162
BC4869 BC4869 Minor extracellular protease VPR precursor (NCBI ptt file) 108, 162
BC4910 BC4910 Exonuclease KapD (NCBI ptt file) 84, 162
BC5071 BC5071 Macrolide-efflux protein (NCBI ptt file) 86, 162
BC5146 BC5146 hypothetical protein (NCBI ptt file) 102, 162
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 BC2457
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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