Organism : Bacillus cereus ATCC14579 | Module List :
BC0405

Arginine repressor, argR (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Arginine repressor cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
argR_whole tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0405
(Mouseover regulator name to see its description)

BC0405 is regulated by 30 influences and regulates 17 modules.
Regulators for BC0405 (30)
Regulator Module Operator
BC0405 187 tf
BC1131 187 tf
BC3062 187 tf
BC3163 187 tf
BC3758 187 tf
BC4076 187 tf
BC4240 187 tf
BC4256 187 tf
BC4425 187 tf
BC4652 187 tf
BC4708 187 tf
BC4902 187 tf
BC5010 187 tf
BC5409 187 tf
BC5481 187 tf
BC0630 100 tf
BC0950 100 tf
BC1850 100 tf
BC1932 100 tf
BC1996 100 tf
BC2122 100 tf
BC2353 100 tf
BC3253 100 tf
BC4010 100 tf
BC4240 100 tf
BC4425 100 tf
BC4826 100 tf
BC4842 100 tf
BC5265 100 tf
BC5402 100 tf

Warning: BC0405 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
4116 1.40e-04 AgaaAaAgGgatgtt
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4117 2.00e+03 GGaGaTacgCC
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4290 7.40e-07 aaaagGA.gAg
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4291 2.40e+04 CGctCTTGCC
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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 BC0405

BC0405 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Arginine repressor cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
argR_whole tigr/ tigrfam
Module neighborhood information for BC0405

BC0405 has total of 53 gene neighbors in modules 100, 187
Gene neighbors (53)
Gene Common Name Description Module membership
BC0052 BC0052 Translation initiation inhibitor (NCBI ptt file) 187, 401
BC0291 BC0291 AT-rich DNA-binding protein (NCBI ptt file) 119, 187
BC0405 BC0405 Arginine repressor, argR (NCBI ptt file) 100, 187
BC1131 BC1131 Cold shock protein (NCBI ptt file) 187, 477
BC1333 BC1333 CBS domain containing protein (NCBI ptt file) 100, 199
BC1386 BC1386 hypothetical protein (NCBI ptt file) 100, 354
BC1463 BC1463 Purine nucleoside phosphorylase (NCBI ptt file) 28, 187
BC1515 BC1515 Nucleoside diphosphate kinase (NCBI ptt file) 187, 227
BC1820 BC1820 Deoxyribose-phosphate aldolase (NCBI ptt file) 187, 401
BC1850 BC1850 Transcriptional regulator (NCBI ptt file) 100, 294
BC1924 BC1924 L-lactate dehydrogenase (NCBI ptt file) 90, 100
BC1996 BC1996 Transcription state regulatory protein abrB (NCBI ptt file) 100, 517
BC2215 BC2215 Mechanosensitive ion channel (NCBI ptt file) 28, 187
BC2261 BC2261 Cobalt-zinc-cadmium resistance protein czcD (NCBI ptt file) 100, 214
BC2263 BC2263 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 100, 354
BC2356 BC2356 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 28, 100
BC2398 BC2398 putative integral membrane protein (NCBI ptt file) 100, 481
BC2442 BC2442 Transcriptional regulator, LuxR family (NCBI ptt file) 184, 187
BC2527 BC2527 CAAX amino terminal protease family (NCBI ptt file) 100, 354
BC2546 BC2546 hypothetical protein (NCBI ptt file) 187, 190
BC2618 BC2618 hydrolase (HAD superfamily) (NCBI ptt file) 100, 401
BC2717 BC2717 hypothetical protein (NCBI ptt file) 100, 337
BC2718 BC2718 hypothetical protein (NCBI ptt file) 100, 337
BC2826 BC2826 Manganese-dependent inorganic pyrophosphatase (NCBI ptt file) 187, 227
BC2921 BC2921 hypothetical protein (NCBI ptt file) 100, 461
BC2988 BC2988 Transcriptional regulator, Cro/CI family (NCBI ptt file) 100, 440
BC2995 BC2995 hypothetical protein (NCBI ptt file) 7, 100
BC3318 BC3318 hypothetical protein (NCBI ptt file) 7, 100
BC3661 BC3661 CcdC protein (NCBI ptt file) 166, 187
BC3665 BC3665 Bacitracin transport permease protein BCRB (NCBI ptt file) 100, 388
BC4046 BC4046 hypothetical protein (NCBI ptt file) 28, 187
BC4062 BC4062 IG hypothetical 17221 (NCBI ptt file) 100, 477
BC4093 BC4093 Ribosomal-protein-serine acetyltransferase (NCBI ptt file) 187, 401
BC4197 BC4197 Protein Translation Elongation Factor P (EF-P) (NCBI ptt file) 187, 350
BC4370 BC4370 hypothetical protein (NCBI ptt file) 100, 477
BC4425 BC4425 hypothetical transcriptional regulator (NCBI ptt file) 28, 187
BC4559 BC4559 Asparaginyl-tRNA synthetase (NCBI ptt file) 100, 412
BC4625 BC4625 Universal stress protein family (NCBI ptt file) 129, 187
BC4664 BC4664 hypothetical protein (NCBI ptt file) 100, 228
BC4675 BC4675 Sex pheromone staph-cAM373 precursor (NCBI ptt file) 7, 100
BC4760 BC4760 Acetyltransferase (NCBI ptt file) 187, 296
BC4826 BC4826 hypothetical protein (NCBI ptt file) 100, 304
BC4842 BC4842 Transcriptional regulator, GntR family (NCBI ptt file) 100, 304
BC4860 BC4860 hypothetical protein (NCBI ptt file) 187, 381
BC4929 BC4929 Macrolide-efflux protein (NCBI ptt file) 20, 100
BC5190 BC5190 Probable Sigma (54) modulation protein / SSU ribosomal protein S30P (NCBI ptt file) 129, 187
BC5258 BC5258 Phosphoglycerate transporter protein (NCBI ptt file) 100, 290
BC5323 BC5323 hypothetical protein (NCBI ptt file) 126, 187
BC5349 BC5349 PapR protein (NCBI ptt file) 100, 354
BC5374 BC5374 Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) 129, 187
BC5378 BC5378 4-oxalocrotonate tautomerase (NCBI ptt file) 187, 401
BC5409 BC5409 Catabolite gene activator (NCBI ptt file) 187, 380
BC5444 BC5444 Nitric oxide synthase (NCBI ptt file) 187, 290
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 BC0405
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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