Organism : Bacillus cereus ATCC14579 | Module List :
BC3127

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 BC3127
(Mouseover regulator name to see its description)

BC3127 is regulated by 25 influences and regulates 4 modules.
Regulators for BC3127 (25)
Regulator Module Operator
BC0356 359 tf
BC0993 359 tf
BC1387 359 tf
BC1537 359 tf
BC2250 359 tf
BC2979 359 tf
BC3069 359 tf
BC3127 359 tf
BC3826 359 tf
BC3922 359 tf
BC4072 359 tf
BC4081 359 tf
BC5265 359 tf
BC5409 359 tf
BC0158 52 tf
BC0213 52 tf
BC1253 52 tf
BC3127 52 tf
BC3313 52 tf
BC3332 52 tf
BC3493 52 tf
BC4181 52 tf
BC4289 52 tf
BC4294 52 tf
BC4508 52 tf

Warning: BC3127 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
4024 4.60e+03 TgGgGGGAA
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4025 2.20e+04 GcACAGcG
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4628 1.60e-01 AaaaAgt.aGG
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4629 5.80e+02 gAgcgGcTTcTTTTt
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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 BC3127

BC3127 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 BC3127

BC3127 has total of 42 gene neighbors in modules 52, 359
Gene neighbors (42)
Gene Common Name Description Module membership
BC0606 BC0606 Vancomycin B-type resistance protein vanW (NCBI ptt file) 52, 280
BC0634 BC0634 Spore germination protein KB (NCBI ptt file) 52, 397
BC0785 BC0785 hypothetical protein (NCBI ptt file) 359, 398
BC0867 BC0867 hypothetical protein (NCBI ptt file) 194, 359
BC0993 BC0993 Transcriptional regulator, PadR family (NCBI ptt file) 299, 359
BC1103 BC1103 hypothetical protein (NCBI ptt file) 52, 150
BC1186 BC1186 hypothetical protein (NCBI ptt file) 52, 284
BC1459 BC1459 hypothetical Cytosolic Protein (NCBI ptt file) 254, 359
BC1537 BC1537 Biotin operon repressor / Biotin--[acetyl-CoA-carboxylase] synthetase (NCBI ptt file) 359, 407
BC1658 BC1658 Flagellin (NCBI ptt file) 52, 238
BC1833 BC1833 hypothetical protein (NCBI ptt file) 52, 253
BC1921 BC1921 Site-specific recombinase (NCBI ptt file) 237, 359
BC1922 BC1922 Glutamyl-tRNA(Gln) amidotransferase subunit A (NCBI ptt file) 237, 359
BC2013 BC2013 Alpha/beta hydrolase (NCBI ptt file) 52, 218
BC2070 BC2070 Serine/threonine protein phosphatase (NCBI ptt file) 359, 377
BC2249 BC2249 Beta-lysine acetyltransferase (NCBI ptt file) 359, 362
BC2250 BC2250 L-lysine aminomutase regulator (NCBI ptt file) 359, 420
BC2609 BC2609 Cytochrome P450 (NCBI ptt file) 299, 359
BC2639 BC2639 Cell surface protein (NCBI ptt file) 359, 391
BC2877 BC2877 Zwittermicin A resistance protein ZmaR (NCBI ptt file) 52, 72
BC2899 BC2899 2'-5' RNA ligase (NCBI ptt file) 52, 218
BC2978 BC2978 Peptidase family M20 (NCBI ptt file) 359, 402
BC3127 BC3127 Transcriptional regulators, LysR family (NCBI ptt file) 52, 359
BC3150 BC3150 Transcriptional regulator, AraC family (NCBI ptt file) 359, 453
BC3205 BC3205 Succinoglycan biosynthesis protein (NCBI ptt file) 26, 52
BC3241 BC3241 Hydrogenase maturation protein hypF (NCBI ptt file) 52, 104
BC3248 BC3248 D-3-phosphoglycerate dehydrogenase (NCBI ptt file) 218, 359
BC3249 BC3249 Phosphoserine aminotransferase (NCBI ptt file) 150, 359
BC3339 BC3339 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 52, 146
BC3346 BC3346 Collagen-like triple helix repeat protein (NCBI ptt file) 359, 512
BC3365 BC3365 hypothetical protein (NCBI ptt file) 72, 359
BC3390 BC3390 Nitroreductase family protein (NCBI ptt file) 52, 402
BC3469 BC3469 hypothetical protein (NCBI ptt file) 299, 359
BC3532 BC3532 Glyoxalase family protein (NCBI ptt file) 359, 407
BC3657 BC3657 4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme (NCBI ptt file) 218, 359
BC4217 BC4217 ABC transporter permease protein (NCBI ptt file) 52, 150
BC4218 BC4218 ABC transporter permease protein (NCBI ptt file) 52, 150
BC4234 BC4234 ComG operon protein 7 (NCBI ptt file) 279, 359
BC4350 BC4350 hypothetical Exported Protein (NCBI ptt file) 52, 253
BC4701 BC4701 2'-5' RNA ligase (NCBI ptt file) 359, 407
BC4976 BC4976 hypothetical protein (NCBI ptt file) 241, 359
BC5014 BC5014 hypothetical exported repetitive protein (NCBI ptt file) 284, 359
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 BC3127
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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