Organism : Bacillus cereus ATCC14579 | Module List :
BC2507

Transcriptional regulator, AraC family (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2507
(Mouseover regulator name to see its description)

BC2507 is regulated by 21 influences and regulates 3 modules.
Regulators for BC2507 (21)
Regulator Module Operator
BC0082 225 tf
BC0473 225 tf
BC0598 225 tf
BC0950 225 tf
BC1915 225 tf
BC2340 225 tf
BC2386 225 tf
BC2794 225 tf
BC3244 225 tf
BC3826 225 tf
BC4652 225 tf
BC1059 263 tf
BC1489 263 tf
BC1531 263 tf
BC1987 263 tf
BC2351 263 tf
BC2401 263 tf
BC2794 263 tf
BC3497 263 tf
BC4930 263 tf
BC5340 263 tf

Warning: BC2507 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
4366 1.80e+04 CATGTGTcAAGcG
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4367 3.60e+03 AAggaGtGaaT
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4442 8.90e+02 aGGaggGAA
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4443 2.20e+03 ATTtCGcCG.aTgAtTCccc
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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 BC2507

BC2507 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for BC2507

BC2507 has total of 69 gene neighbors in modules 225, 263
Gene neighbors (69)
Gene Common Name Description Module membership
BC0012 BC0012 IG hypothetical 16768 (NCBI ptt file) 137, 225
BC0035 BC0035 Arginine decarboxylase (NCBI ptt file) 263, 308
BC0044 BC0044 Sec-independent secretion protein tatD (NCBI ptt file) 72, 225
BC0048 BC0048 VEG protein (NCBI ptt file) 225, 285
BC0189 BC0189 hypothetical protein (NCBI ptt file) 175, 263
BC0231 BC0231 hypothetical protein (NCBI ptt file) 225, 353
BC0254 BC0254 Homogentisate 1,2-dioxygenase (NCBI ptt file) 243, 263
BC0312 BC0312 UDP-glucose 4-epimerase (NCBI ptt file) 9, 263
BC0391 BC0391 hypothetical protein (NCBI ptt file) 263, 351
BC0413 BC0413 Exo-alpha-1,4-glucosidase (NCBI ptt file) 225, 294
BC0603 BC0603 hypothetical Membrane Spanning Protein (NCBI ptt file) 225, 465
BC0664 BC0664 None 224, 263
BC0836 BC0836 None 31, 225
BC0876 BC0876 hypothetical protein (NCBI ptt file) 86, 263
BC0900 BC0900 hypothetical protein (NCBI ptt file) 199, 225
BC0974 BC0974 hypothetical protein (NCBI ptt file) 225, 288
BC1050 BC1050 ABC-type transporter ATP-binding protein ecsA (NCBI ptt file) 263, 416
BC1132 BC1132 hypothetical protein (NCBI ptt file) 141, 263
BC1140 BC1140 Spore germination protein PF (NCBI ptt file) 263, 288
BC1144 BC1144 Spore germination protein PB (NCBI ptt file) 56, 263
BC1145 BC1145 Spore germination protein PA (NCBI ptt file) 26, 263
BC1176 BC1176 hypothetical protein (NCBI ptt file) 263, 284
BC1478 BC1478 Sensor protein resE (NCBI ptt file) 193, 263
BC1556 BC1556 hypothetical protein (NCBI ptt file) 263, 343
BC1616 BC1616 hypothetical Membrane Associated Protein (NCBI ptt file) 225, 487
BC1713 BC1713 hypothetical Membrane Spanning Protein (NCBI ptt file) 171, 225
BC1714 BC1714 hypothetical protein (NCBI ptt file) 186, 225
BC1772 BC1772 Beta-lactamase inhibitory protein II (NCBI ptt file) 26, 263
BC2015 BC2015 hypothetical protein (NCBI ptt file) 225, 228
BC2020 BC2020 Spermine/spermidine acetyltransferase (NCBI ptt file) 175, 225
BC2037 BC2037 hypothetical Membrane Spanning Protein (NCBI ptt file) 263, 329
BC2040 BC2040 putative spore coat protein (NCBI ptt file) 146, 225
BC2115 BC2115 Transglutaminase-like enzymes, hypothetical cysteine proteases (NCBI ptt file) 9, 225
BC2190 BC2190 Penicillin-binding protein (NCBI ptt file) 225, 299
BC2226 BC2226 hypothetical protein (NCBI ptt file) 225, 299
BC2275 BC2275 hypothetical cytosolic protein pX02-70 (NCBI ptt file) 263, 457
BC2298 BC2298 Transcriptional repressor (NCBI ptt file) 146, 225
BC2351 BC2351 Transcriptional regulator, MerR family (NCBI ptt file) 263, 449
BC2428 BC2428 hypothetical protein (NCBI ptt file) 63, 225
BC2476 BC2476 phosphoesterase (NCBI ptt file) 263, 449
BC2507 BC2507 Transcriptional regulator, AraC family (NCBI ptt file) 225, 263
BC2604 BC2604 hypothetical Membrane Spanning Protein (NCBI ptt file) 263, 389
BC2606 BC2606 hypothetical Membrane Spanning Protein (NCBI ptt file) 225, 416
BC2663 BC2663 None 218, 225
BC2673 BC2673 Tetracycline resistance determinant tetV (NCBI ptt file) 263, 465
BC2687 BC2687 hypothetical protein (NCBI ptt file) 127, 263
BC3040 BC3040 EMG2 protein (NCBI ptt file) 97, 225
BC3236 BC3236 hypothetical Cytosolic Protein (NCBI ptt file) 225, 468
BC3452 BC3452 hypothetical protein (NCBI ptt file) 199, 225
BC3560 BC3560 hypothetical Membrane Spanning Protein (NCBI ptt file) 222, 263
BC3622 BC3622 Multidrug resistance protein B (NCBI ptt file) 263, 468
BC3715 BC3715 hypothetical protein (NCBI ptt file) 225, 397
BC3720 BC3720 Fructose repressor (NCBI ptt file) 234, 263
BC3739 BC3739 Exodeoxyribonuclease III (NCBI ptt file) 225, 416
BC3763 BC3763 None 225, 485
BC3897 BC3897 RNA binding protein (NCBI ptt file) 263, 281
BC4002 BC4002 hypothetical protein (NCBI ptt file) 225, 334
BC4236 BC4236 ComG operon protein 4 (NCBI ptt file) 263, 321
BC4257 BC4257 hypothetical Cytosolic Protein (NCBI ptt file) 194, 225
BC4416 BC4416 Ferrichrome-binding protein (NCBI ptt file) 263, 449
BC4564 BC4564 Metal-dependent phosphohydrolase (NCBI ptt file) 89, 225
BC4572 BC4572 hypothetical Cytosolic Protein (NCBI ptt file) 263, 455
BC4582 BC4582 S-adenosylmethionine decarboxylase proenzyme (NCBI ptt file) 225, 265
BC4809 BC4809 Two component system histidine kinase (NCBI ptt file) 263, 449
BC4810 BC4810 Two-component response regulator (NCBI ptt file) 242, 263
BC4819 BC4819 hypothetical protein (NCBI ptt file) 263, 414
BC5214 BC5214 S-adenosylmethionine decarboxylase proenzyme (NCBI ptt file) 138, 225
BC5216 BC5216 PTS system, lichenan oligosaccharide-specific IIC component (NCBI ptt file) 127, 263
BC5448 BC5448 UDP-glucose 4-epimerase (NCBI ptt file) 146, 263
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 BC2507
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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