Organism : Bacillus cereus ATCC14579 | Module List :
BC1363

Leucine-responsive regulatory protein (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulators cog/ cog
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 BC1363
(Mouseover regulator name to see its description)

BC1363 is regulated by 19 influences and regulates 49 modules.
Regulators for BC1363 (19)
Regulator Module Operator
BC0613 204 tf
BC0954 204 tf
BC1363 204 tf
BC1841 204 tf
BC2218 204 tf
BC2434 204 tf
BC4072 204 tf
BC5000 204 tf
BC5256 204 tf
BC0099 428 tf
BC0975 428 tf
BC1363 428 tf
BC2122 428 tf
BC2218 428 tf
BC2386 428 tf
BC2526 428 tf
BC2742 428 tf
BC3175 428 tf
BC5175 428 tf

Warning: BC1363 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
4324 1.20e-05 aGgAGgagaAa
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4325 2.50e+03 TAaAagGGAA
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4766 5.50e-07 aataaaaGgAG
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4767 4.70e+03 GgacGgGaga
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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 BC1363

BC1363 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcriptional regulators cog/ cog
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 BC1363

BC1363 has total of 55 gene neighbors in modules 204, 428
Gene neighbors (55)
Gene Common Name Description Module membership
BC0171 BC0171 Chitooligosaccharide deacetylase (NCBI ptt file) 158, 428
BC0203 BC0203 hypothetical protein (NCBI ptt file) 204, 340
BC0436 BC0436 Permease (NCBI ptt file) 58, 204
BC0629 BC0629 Arginine/ornithine antiporter (NCBI ptt file) 134, 428
BC1124 BC1124 Methyl-accepting chemotaxis protein (NCBI ptt file) 428, 489
BC1254 BC1254 hypothetical protein (NCBI ptt file) 9, 428
BC1309 BC1309 TerC-like protein (NCBI ptt file) 204, 410
BC1363 BC1363 Leucine-responsive regulatory protein (NCBI ptt file) 204, 428
BC1571 BC1571 hypothetical Membrane Spanning Protein (NCBI ptt file) 204, 214
BC1577 BC1577 hypothetical protein (NCBI ptt file) 428, 481
BC1654 BC1654 Chemotaxis protein cheV (NCBI ptt file) 157, 428
BC1676 BC1676 hypothetical protein (NCBI ptt file) 312, 428
BC1677 BC1677 Dienelactone hydrolase family (NCBI ptt file) 141, 428
BC1709 BC1709 malate-2H+/lactate-NA+ antiporter (NCBI ptt file) 67, 204
BC1752 BC1752 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 214, 428
BC1767 BC1767 Sodium-dependent serine transporter (NCBI ptt file) 412, 428
BC2059 BC2059 Phosphoglycerate mutase (NCBI ptt file) 62, 428
BC2060 BC2060 hydrolase (HAD superfamily) (NCBI ptt file) 62, 428
BC2061 BC2061 Multidrug resistance protein B (NCBI ptt file) 256, 428
BC2399 BC2399 Serine--pyruvate aminotransferase (NCBI ptt file) 204, 341
BC2400 BC2400 Threonine dehydratase (NCBI ptt file) 204, 341
BC2526 BC2526 Transcriptional regulator, GntR family (NCBI ptt file) 30, 428
BC2627 BC2627 hypothetical protein (NCBI ptt file) 150, 204
BC2628 BC2628 hypothetical protein (NCBI ptt file) 150, 204
BC2699 BC2699 None 139, 428
BC2900 BC2900 CcdC protein (NCBI ptt file) 204, 341
BC2901 BC2901 ABC transporter permease protein (NCBI ptt file) 30, 204
BC3121 BC3121 5'-nucleotidase (NCBI ptt file) 214, 428
BC3146 BC3146 Peptidoglycan N-acetylglucosamine deacetylase (NCBI ptt file) 9, 428
BC3175 BC3175 Leucine-responsive regulatory protein (NCBI ptt file) 364, 428
BC3210 BC3210 hypothetical Cytosolic Protein (NCBI ptt file) 312, 428
BC3251 BC3251 hypothetical protein (NCBI ptt file) 204, 410
BC3446 BC3446 hypothetical protein (NCBI ptt file) 428, 453
BC3506 BC3506 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 246, 428
BC3507 BC3507 hypothetical protein (NCBI ptt file) 428, 481
BC3639 BC3639 hypothetical Membrane Spanning Protein (NCBI ptt file) 214, 428
BC4216 BC4216 hypothetical protein (NCBI ptt file) 341, 428
BC4352 BC4352 Phenylalanine-4-hydroxylase (NCBI ptt file) 158, 428
BC4812 BC4812 Cell surface protein (NCBI ptt file) 158, 428
BC5117 BC5117 ABC transporter permease protein (NCBI ptt file) 204, 410
BC5118 BC5118 ABC transporter ATP-binding protein (NCBI ptt file) 204, 410
BC5119 BC5119 hypothetical protein (NCBI ptt file) 204, 410
BC5120 BC5120 hypothetical Cytosolic Protein (NCBI ptt file) 204, 410
BC5121 BC5121 hypothetical protein (NCBI ptt file) 204, 410
BC5122 BC5122 hypothetical Cytosolic Protein (NCBI ptt file) 204, 410
BC5123 BC5123 hypothetical protein (NCBI ptt file) 204, 410
BC5124 BC5124 hypothetical protein (NCBI ptt file) 204, 410
BC5125 BC5125 hypothetical protein (NCBI ptt file) 204, 410
BC5237 BC5237 N-acetylglucosaminyltransferase (NCBI ptt file) 204, 431
BC5241 BC5241 IG hypothetical 16680 (NCBI ptt file) 204, 410
BC5242 BC5242 Membrane protein with C2C2 zinc finger (NCBI ptt file) 62, 204
BC5243 BC5243 hypothetical protein (NCBI ptt file) 204, 410
BC5263 BC5263 UDP-glucose 4-epimerase (NCBI ptt file) 204, 214
BC5389 BC5389 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 133, 204
BC5428 BC5428 hypothetical protein (NCBI ptt file) 341, 428
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 BC1363
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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