Organism : Bacillus cereus ATCC14579 | Module List :
BC3253

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 BC3253
(Mouseover regulator name to see its description)

BC3253 is regulated by 25 influences and regulates 18 modules.
Regulators for BC3253 (25)
Regulator Module Operator
BC0583 427 tf
BC0758 427 tf
BC0993 427 tf
BC2794 427 tf
BC2936 427 tf
BC3190 427 tf
BC3253 427 tf
BC3476 427 tf
BC3497 427 tf
BC4053 427 tf
BC4072 427 tf
BC4101 427 tf
BC4174 427 tf
BC5205 427 tf
BC5265 427 tf
BC1673 407 tf
BC2358 407 tf
BC3253 407 tf
BC3476 407 tf
BC3720 407 tf
BC4053 407 tf
BC4425 407 tf
BC5205 407 tf
BC5402 407 tf
BC5409 407 tf

Warning: BC3253 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
4724 3.80e-02 gaaaaaGaaGGgGAa
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4725 1.60e+03 Ggg.AGCgG
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4764 1.50e-05 aAaGgAGa.Gg
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4765 1.50e+04 GCAGCTGC
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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 BC3253

BC3253 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 BC3253

BC3253 has total of 60 gene neighbors in modules 407, 427
Gene neighbors (60)
Gene Common Name Description Module membership
BC0638 BC0638 Sodium/proton-dependent alanine carrier protein (NCBI ptt file) 339, 407
BC0761 BC0761 ABC transporter permease protein (NCBI ptt file) 286, 427
BC0762 BC0762 hypothetical protein (NCBI ptt file) 286, 427
BC0763 BC0763 ABC transporter permease protein (NCBI ptt file) 286, 427
BC0964 BC0964 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 280, 407
BC1098 BC1098 hypothetical protein (NCBI ptt file) 286, 427
BC1100 BC1100 hypothetical protein (NCBI ptt file) 208, 427
BC1112 BC1112 Metal-dependent phosphohydrolase (NCBI ptt file) 56, 407
BC1142 BC1142 Spore germination protein PD (NCBI ptt file) 351, 407
BC1170 BC1170 putative hydrolase (NCBI ptt file) 76, 407
BC1258 BC1258 hypothetical protein (NCBI ptt file) 63, 427
BC1269 BC1269 hypothetical protein (NCBI ptt file) 286, 427
BC1407 BC1407 Imidazoleglycerol-phosphate dehydratase (NCBI ptt file) 301, 407
BC1413 BC1413 histidinol-phosphatase (RefSeq) 301, 407
BC1529 BC1529 DNA polymerase, bacteriophage-type (NCBI ptt file) 407, 446
BC1537 BC1537 Biotin operon repressor / Biotin--[acetyl-CoA-carboxylase] synthetase (NCBI ptt file) 359, 407
BC1568 BC1568 Methionine aminopeptidase (NCBI ptt file) 217, 407
BC1584 BC1584 Capsular polysaccharide protein CpsC (NCBI ptt file) 370, 427
BC1585 BC1585 Tyrosine-protein kinase cpsD (NCBI ptt file) 370, 427
BC1586 BC1586 Undecaprenyl-phosphate galactosephosphotransferase (NCBI ptt file) 370, 427
BC1587 BC1587 Oligosaccharide translocase (flippase) (NCBI ptt file) 370, 427
BC1588 BC1588 Secreted polysaccharide polymerase (NCBI ptt file) 286, 427
BC1785 BC1785 Acetyltransferase (NCBI ptt file) 258, 427
BC2054 BC2054 Glutamyl-tRNA(Gln) amidotransferase subunit A (NCBI ptt file) 146, 427
BC2188 BC2188 hypothetical protein (NCBI ptt file) 427, 439
BC2189 BC2189 Aminoglycoside phosphotransferase (NCBI ptt file) 209, 407
BC2406 BC2406 Metal-dependent hydrolase (NCBI ptt file) 113, 427
BC2414 BC2414 Phage protein (NCBI ptt file) 150, 407
BC2510 BC2510 Collagen adhesion protein (NCBI ptt file) 104, 407
BC2532 BC2532 Methyltransferase (NCBI ptt file) 56, 427
BC2602 BC2602 hypothetical protein (NCBI ptt file) 154, 407
BC2686 BC2686 MutT/nudix family protein (NCBI ptt file) 47, 427
BC2776 BC2776 Dihydrolipoamide dehydrogenase (NCBI ptt file) 146, 427
BC2777 BC2777 Dihydrolipoamide acetyltransferase component of acetoin dehydrogenase complex (NCBI ptt file) 355, 407
BC2822 BC2822 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 361, 427
BC3164 BC3164 Xanthine dehydrogenase (molybdopterin-guanine dinucleotide biosynthesis subunit) (NCBI ptt file) 347, 407
BC3165 BC3165 Xanthine dehydrogenase subunit (NCBI ptt file) 347, 407
BC3166 BC3166 Xanthine dehydrogenase iron-sulfur subunit (NCBI ptt file) 407, 484
BC3178 BC3178 Lactoylglutathione lyase (NCBI ptt file) 287, 407
BC3190 BC3190 Transcriptional regulators, LysR family (NCBI ptt file) 56, 407
BC3233 BC3233 Glucose/mannose transporter (NCBI ptt file) 347, 407
BC3246 BC3246 hypothetical protein (NCBI ptt file) 72, 427
BC3253 BC3253 Transcriptional regulator, AraC family (NCBI ptt file) 407, 427
BC3459 BC3459 hypothetical protein (NCBI ptt file) 56, 407
BC3476 BC3476 Transcriptional regulators, LysR family (NCBI ptt file) 72, 407
BC3532 BC3532 Glyoxalase family protein (NCBI ptt file) 359, 407
BC3544 BC3544 hypothetical Cytosolic Protein (NCBI ptt file) 370, 427
BC3590 BC3590 ABC transporter permease protein (NCBI ptt file) 330, 427
BC3591 BC3591 ABC transporter ATP-binding protein (NCBI ptt file) 330, 427
BC3638 BC3638 Serine/threonine protein phosphatase (NCBI ptt file) 377, 407
BC3646 BC3646 Ferredoxin-dependent glutamate synthase (NCBI ptt file) 358, 407
BC3658 BC3658 hypothetical ATP-binding protein (NCBI ptt file) 154, 427
BC3800 BC3800 Dipicolinate synthase, B chain (NCBI ptt file) 393, 407
BC3801 BC3801 Dipicolinate synthase, A chain (NCBI ptt file) 76, 407
BC3857 BC3857 Thiamin pyrophosphokinase (NCBI ptt file) 347, 407
BC4606 BC4606 hypothetical Membrane Spanning Protein (NCBI ptt file) 84, 407
BC4643 BC4643 Metal-dependent hydrolase (NCBI ptt file) 407, 427
BC4701 BC4701 2'-5' RNA ligase (NCBI ptt file) 359, 407
BC4729 BC4729 hypothetical protein (NCBI ptt file) 286, 427
BC5436 BC5436 Peptide methionine sulfoxide reductase (NCBI ptt file) 72, 427
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 BC3253
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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