Organism : Bacillus cereus ATCC14579 | Module List :
BC3668

Transcriptional regulators, LysR family (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3668
(Mouseover regulator name to see its description)

BC3668 is regulated by 26 influences and regulates 12 modules.
Regulators for BC3668 (26)
Regulator Module Operator
BC0498 6 tf
BC0586 6 tf
BC1818 6 tf
BC1889 6 tf
BC1987 6 tf
BC2340 6 tf
BC2367 6 tf
BC2401 6 tf
BC2410 6 tf
BC2469 6 tf
BC3072 6 tf
BC3668 6 tf
BC5097 6 tf
BC5200 6 tf
BC5340 6 tf
BC0586 261 tf
BC0840 261 tf
BC1053 261 tf
BC1614 261 tf
BC3668 261 tf
BC3976 261 tf
BC4091 261 tf
BC4204 261 tf
BC4581 261 tf
BC4589 261 tf
BC5340 261 tf

Warning: BC3668 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
3934 3.40e-06 ggaAGGaG
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3935 1.00e+03 TCggaaagcccgtaaAaGcccG
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4438 1.20e+01 taaTatgAcaAgaaaagAGgga
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4439 2.80e+04 GcACACcC
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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 BC3668

BC3668 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC3668

BC3668 has total of 50 gene neighbors in modules 6, 261
Gene neighbors (50)
Gene Common Name Description Module membership
BC0388 BC0388 hypothetical protein (NCBI ptt file) 261, 449
BC0393 BC0393 Sporulation kinase (NCBI ptt file) 261, 438
BC0394 BC0394 hypothetical protein (NCBI ptt file) 261, 265
BC0628 BC0628 Sensory box/GGDEF family protein (NCBI ptt file) 6, 260
BC0689 BC0689 Guanine-hypoxanthine permease (NCBI ptt file) 6, 148
BC0839 BC0839 hypothetical protein (NCBI ptt file) 261, 449
BC0840 BC0840 Transcriptional regulator, RpiR family (NCBI ptt file) 41, 261
BC0921 BC0921 hypothetical protein (NCBI ptt file) 6, 442
BC1043 BC1043 Protein export protein prsA precursor (NCBI ptt file) 6, 442
BC1044 BC1044 hypothetical protein (NCBI ptt file) 6, 260
BC1276 BC1276 hypothetical protein (NCBI ptt file) 6, 260
BC1298 BC1298 Carbohydrate diacid regulator (NCBI ptt file) 41, 261
BC1336 BC1336 Sporulation kinase D (NCBI ptt file) 6, 440
BC1458 BC1458 Sporulation kinase (NCBI ptt file) 6, 170
BC1513 BC1513 2-heptaprenyl-1,4-naphthoquinone methyltransferase (NCBI ptt file) 6, 260
BC1528 BC1528 hypothetical Membrane Spanning Protein (NCBI ptt file) 261, 507
BC1614 BC1614 Multidrug-efflux transporter 2 regulator (NCBI ptt file) 261, 414
BC1718 BC1718 hypothetical protein (NCBI ptt file) 228, 261
BC1720 BC1720 Cell surface protein (NCBI ptt file) 261, 265
BC1768 BC1768 Chitooligosaccharide deacetylase (NCBI ptt file) 6, 170
BC1818 BC1818 Transcriptional regulator, TetR family (NCBI ptt file) 6, 273
BC1990 BC1990 hypothetical Cytosolic Protein (NCBI ptt file) 6, 249
BC2180 BC2180 hypothetical protein (NCBI ptt file) 6, 79
BC2241 BC2241 Succinate-semialdehyde dehydrogenase [NADP+] (NCBI ptt file) 6, 511
BC2280 BC2280 hypothetical Membrane Spanning Protein (NCBI ptt file) 6, 304
BC2364 BC2364 hypothetical protein (NCBI ptt file) 6, 20
BC2539 BC2539 Two-component sensor kinase yxdK (NCBI ptt file) 6, 63
BC2657 BC2657 None 6, 180
BC2733 BC2733 hypothetical protein (NCBI ptt file) 6, 254
BC2740 BC2740 Protein translocase subunit SecY (NCBI ptt file) 6, 63
BC2797 BC2797 Acetyltransferase (NCBI ptt file) 6, 20
BC3200 BC3200 Two-component response regulator (NCBI ptt file) 6, 449
BC3201 BC3201 Two component system histidine kinase (NCBI ptt file) 6, 455
BC3535 BC3535 IG hypothetical 17116 (NCBI ptt file) 6, 170
BC3611 BC3611 DNA polymerase III alpha subunit (NCBI ptt file) 41, 261
BC3641 BC3641 Sensor protein atoS (NCBI ptt file) 6, 260
BC3668 BC3668 Transcriptional regulators, LysR family (NCBI ptt file) 6, 261
BC3949 BC3949 hypothetical protein (NCBI ptt file) 81, 261
BC4102 BC4102 Alpha/beta hydrolase (NCBI ptt file) 6, 208
BC4247 BC4247 hypothetical protein (NCBI ptt file) 6, 55
BC4323 BC4323 ComE operon protein 2 (NCBI ptt file) 261, 385
BC4334 BC4334 hypothetical protein (NCBI ptt file) 261, 449
BC4505 BC4505 Transcriptional regulator (NCBI ptt file) 41, 261
BC4562 BC4562 23S rRNA methyltransferase (NCBI ptt file) 41, 261
BC4581 BC4581 putative regulatory protein (NCBI ptt file) 118, 261
BC4588 BC4588 Phosphate regulon sensor protein phoR (NCBI ptt file) 261, 527
BC5028 BC5028 Two-component response regulator vanRB (NCBI ptt file) 6, 41
BC5130 BC5130 Carboxylesterase (NCBI ptt file) 261, 505
BC5199 BC5199 Xaa-Pro dipeptidase (NCBI ptt file) 261, 385
BC5373 BC5373 Transcriptional regulator, MerR family (NCBI ptt file) 261, 505
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 BC3668
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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