Organism : Bacillus cereus ATCC14579 | Module List :
BC0224

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 BC0224
(Mouseover regulator name to see its description)

BC0224 is regulated by 25 influences and regulates 18 modules.
Regulators for BC0224 (25)
Regulator Module Operator
BC0224 443 tf
BC0266 443 tf
BC0435 443 tf
BC1282 443 tf
BC3704 443 tf
BC4174 443 tf
BC4256 443 tf
BC4499 443 tf
BC4826 443 tf
BC5205 443 tf
BC5339 443 tf
BC5434 443 tf
BC0224 221 tf
BC0953 221 tf
BC1080 221 tf
BC1363 221 tf
BC1819 221 tf
BC1889 221 tf
BC2410 221 tf
BC2514 221 tf
BC2770 221 tf
BC2773 221 tf
BC3868 221 tf
BC3982 221 tf
BC5205 221 tf

Warning: BC0224 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
4358 5.00e-01 AGGggGag
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4359 8.10e+02 TGc.GTGAG
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4796 4.70e+03 GcGAGCGC
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4797 1.10e+04 CTCACCGC
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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 BC0224

BC0224 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 BC0224

BC0224 has total of 35 gene neighbors in modules 221, 443
Gene neighbors (35)
Gene Common Name Description Module membership
BC0224 BC0224 Transcriptional regulators, LysR family (NCBI ptt file) 221, 443
BC0435 BC0435 Transcriptional regulator, PBSX family (NCBI ptt file) 103, 443
BC0458 BC0458 Alkaline phosphatase like protein (NCBI ptt file) 354, 443
BC0459 BC0459 Bacterial/Archaeal Transporter family protein (NCBI ptt file) 304, 443
BC0517 BC0517 Thioredoxin-dependent thiol peroxidase (NCBI ptt file) 243, 443
BC0616 BC0616 Iron(III) dicitrate-binding protein (NCBI ptt file) 7, 443
BC0656 BC0656 Glycerol-3-phosphate transporter (NCBI ptt file) 221, 479
BC0786 BC0786 Nitroreductase family (NCBI ptt file) 389, 443
BC0995 BC0995 hypothetical protein (NCBI ptt file) 343, 443
BC1151 BC1151 IG hypothetical 17028 (NCBI ptt file) 414, 443
BC1617 BC1617 hypothetical Cytosolic Protein (NCBI ptt file) 257, 443
BC1620 BC1620 hypothetical membrane protein (NCBI ptt file) 221, 304
BC1648 BC1648 hypothetical Cytosolic Protein (NCBI ptt file) 88, 221
BC1974 BC1974 Peptidoglycan N-acetylglucosamine deacetylase (NCBI ptt file) 221, 461
BC2045 BC2045 hypothetical protein (NCBI ptt file) 228, 443
BC2193 BC2193 MecA protein (NCBI ptt file) 193, 221
BC2195 BC2195 1-acyl-sn-glycerol-3-phosphate acyltransferase (NCBI ptt file) 88, 221
BC2376 BC2376 hypothetical protein (NCBI ptt file) 221, 312
BC2690 BC2690 Quaternary ammonium compound-resistance protein (NCBI ptt file) 443, 468
BC3577 BC3577 Amino acid permease (NCBI ptt file) 389, 443
BC3704 BC3704 LexA repressor (NCBI ptt file) 414, 443
BC4108 BC4108 hypothetical protein (NCBI ptt file) 354, 443
BC4337 BC4337 hypothetical Membrane Spanning Protein (NCBI ptt file) 440, 443
BC4344 BC4344 Acetyltransferase (NCBI ptt file) 221, 346
BC4345 BC4345 Lipase (NCBI ptt file) 221, 443
BC4351 BC4351 Minor extracellular protease VPR precursor (NCBI ptt file) 221, 461
BC4511 BC4511 Acid phosphatase (NCBI ptt file) 221, 257
BC4795 BC4795 hypothetical Membrane Spanning Protein (NCBI ptt file) 133, 221
BC4957 BC4957 hypothetical protein (NCBI ptt file) 343, 443
BC5020 BC5020 hypothetical protein (NCBI ptt file) 221, 354
BC5153 BC5153 Catabolite repression protein crh (NCBI ptt file) 221, 374
BC5249 BC5249 hypothetical protein (NCBI ptt file) 354, 443
BC5381 BC5381 Ferrichrome transport ATP-binding protein fhuC (NCBI ptt file) 389, 443
BC5434 BC5434 Transcriptional regulator, TetR family (NCBI ptt file) 222, 443
BC5478 BC5478 hypothetical Cytosolic Protein (NCBI ptt file) 281, 443
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 BC0224
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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