Organism : Bacillus cereus ATCC14579 | Module List :
BC0477

Transcriptional regulator (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Uncharacterized conserved protein cog/ cog
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0477
(Mouseover regulator name to see its description)

BC0477 is regulated by 19 influences and regulates 19 modules.
Regulators for BC0477 (19)
Regulator Module Operator
BC0477 272 tf
BC1851 272 tf
BC2680 272 tf
BC2964 272 tf
BC3332 272 tf
BC3982 272 tf
BC4336 272 tf
BC0477 459 tf
BC0647 459 tf
BC0648 459 tf
BC1329 459 tf
BC2469 459 tf
BC2517 459 tf
BC2680 459 tf
BC2837 459 tf
BC2964 459 tf
BC3903 459 tf
BC5251 459 tf
BC5282 459 tf

Warning: BC0477 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
4460 3.70e-12 aAGGGGg
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4461 2.20e+04 GGACGcAC
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4828 2.30e-02 AAAAg.GagGaa
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4829 1.00e+02 cCCtCc
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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 BC0477

BC0477 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Uncharacterized conserved protein cog/ cog
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for BC0477

BC0477 has total of 38 gene neighbors in modules 272, 459
Gene neighbors (38)
Gene Common Name Description Module membership
BC0261 BC0261 hypothetical membrane protein (Rhomboid family) (NCBI ptt file) 272, 415
BC0308 BC0308 Glycosyltransferase (NCBI ptt file) 272, 487
BC0309 BC0309 Methyltransferase (NCBI ptt file) 272, 339
BC0310 BC0310 Methyltransferase (NCBI ptt file) 272, 487
BC0477 BC0477 Transcriptional regulator (NCBI ptt file) 272, 459
BC0688 BC0688 Proline-specific permease (NCBI ptt file) 272, 405
BC0714 BC0714 Acriflavin resistance plasma membrane protein (NCBI ptt file) 248, 272
BC0861 BC0861 hypothetical protein (NCBI ptt file) 272, 378
BC1249 BC1249 hypothetical Cytosolic Protein (NCBI ptt file) 181, 272
BC1397 BC1397 None 272, 282
BC1445 BC1445 hypothetical protein (NCBI ptt file) 186, 272
BC1608 BC1608 hypothetical Membrane Spanning Protein (NCBI ptt file) 289, 459
BC1894 BC1894 Phage protein (NCBI ptt file) 272, 334
BC2255 BC2255 hypothetical protein (NCBI ptt file) 272, 340
BC2285 BC2285 2-methylcitrate synthase (NCBI ptt file) 232, 459
BC2287 BC2287 Methylisocitrate lyase (NCBI ptt file) 355, 459
BC2316 BC2316 Thermitase (NCBI ptt file) 289, 459
BC2383 BC2383 Oxalate decarboxylase (NCBI ptt file) 272, 334
BC2477 BC2477 hypothetical protein (NCBI ptt file) 196, 272
BC2572 BC2572 Phage protein (NCBI ptt file) 355, 459
BC2608 BC2608 hypothetical Cytosolic Protein (NCBI ptt file) 31, 459
BC2647 BC2647 hypothetical protein (NCBI ptt file) 186, 459
BC2678 BC2678 hypothetical protein (NCBI ptt file) 339, 459
BC2683 BC2683 Inosine-uridine preferring nucleoside hydrolase (NCBI ptt file) 104, 272
BC2751 BC2751 IG hypothetical 17041 (NCBI ptt file) 253, 459
BC2752 BC2752 hypothetical Membrane Spanning Protein (NCBI ptt file) 128, 459
BC2753 BC2753 Cell wall hydrolase cwlJ (NCBI ptt file) 334, 459
BC2754 BC2754 hypothetical protein (NCBI ptt file) 46, 459
BC2816 BC2816 hypothetical protein (NCBI ptt file) 174, 272
BC2980 BC2980 Arginine permease (NCBI ptt file) 294, 459
BC3332 BC3332 Transcriptional regulator, PBSX family (NCBI ptt file) 248, 272
BC3403 BC3403 hypothetical protein (NCBI ptt file) 131, 459
BC3725 BC3725 Exochitinase (NCBI ptt file) 272, 289
BC4304 BC4304 hypothetical Cytosolic Protein (NCBI ptt file) 217, 272
BC4409 BC4409 hypothetical protein (NCBI ptt file) 128, 272
BC4764 BC4764 hypothetical protein (NCBI ptt file) 272, 378
BC5147 BC5147 Stage V sporulation protein AC (NCBI ptt file) 102, 272
BC5480 BC5480 hypothetical protein (NCBI ptt file) 131, 272
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 BC0477
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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