Organism : Bacillus cereus ATCC14579 | Module List :
BC0742

Transcriptional activator tenA (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Putative transcription activator cog/ cog
thiaminase activity go/ molecular_function
Thiamine metabolism kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0742
(Mouseover regulator name to see its description)

BC0742 is regulated by 32 influences and regulates 43 modules.
Regulators for BC0742 (32)
Regulator Module Operator
BC0742 32 tf
BC0848 32 tf
BC1004 32 tf
BC1673 32 tf
BC2401 32 tf
BC2837 32 tf
BC3539 32 tf
BC4081 32 tf
BC4826 32 tf
BC5176 32 tf
BC5409 32 tf
BC0742 3 tf
BC0840 3 tf
BC0848 3 tf
BC0980 3 tf
BC1003 3 tf
BC1131 3 tf
BC1134 3 tf
BC1884 3 tf
BC1915 3 tf
BC2217 3 tf
BC2386 3 tf
BC2442 3 tf
BC2558 3 tf
BC2936 3 tf
BC3690 3 tf
BC4256 3 tf
BC4652 3 tf
BC4703 3 tf
BC4859 3 tf
BC4902 3 tf
BC5176 3 tf

Warning: BC0742 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
3928 3.40e-01 aGGGgA.AGa
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3929 4.40e+01 GG.GGcccg
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3986 5.70e+01 GAaGgGgAaag
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3987 9.10e+02 CaggAaaaggTGTag
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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 BC0742

BC0742 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Putative transcription activator cog/ cog
thiaminase activity go/ molecular_function
Thiamine metabolism kegg/ kegg pathway
Module neighborhood information for BC0742

BC0742 has total of 33 gene neighbors in modules 3, 32
Gene neighbors (33)
Gene Common Name Description Module membership
BC0742 BC0742 Transcriptional activator tenA (NCBI ptt file) 3, 32
BC0743 BC0743 Hydroxymethylpyrimidine transport ATP-binding protein (NCBI ptt file) 3, 301
BC0744 BC0744 Hydroxymethylpyrimidine transport system permease protein (NCBI ptt file) 3, 32
BC0745 BC0745 Hydroxymethylpyrimidine-binding protein (NCBI ptt file) 3, 38
BC0746 BC0746 Regulatory protein TENI (NCBI ptt file) 3, 202
BC0747 BC0747 Glycine oxidase (NCBI ptt file) 3, 32
BC0748 BC0748 ThiS protein (NCBI ptt file) 3, 32
BC0749 BC0749 Thiazole biosynthesis protein thiG (NCBI ptt file) 3, 32
BC0750 BC0750 Molybdopterin biosynthesis MoeB protein (NCBI ptt file) 3, 32
BC0751 BC0751 Phosphomethylpyrimidine kinase (NCBI ptt file) 3, 32
BC0905 BC0905 Proline racemase (NCBI ptt file) 3, 436
BC0906 BC0906 Ornithine cyclodeaminase (NCBI ptt file) 3, 436
BC1398 BC1398 Acetolactate synthase small subunit (NCBI ptt file) 32, 282
BC1399 BC1399 Ketol-acid reductoisomerase (NCBI ptt file) 32, 244
BC1400 BC1400 2-isopropylmalate synthase (NCBI ptt file) 32, 282
BC1402 BC1402 3-isopropylmalate dehydratase large subunit (NCBI ptt file) 32, 463
BC1403 BC1403 3-isopropylmalate dehydratase small subunit (NCBI ptt file) 32, 244
BC1405 BC1405 ATP phosphoribosyltransferase (NCBI ptt file) 3, 32
BC1406 BC1406 Histidinol dehydrogenase (NCBI ptt file) 3, 32
BC1408 BC1408 Amidotransferase hisH (NCBI ptt file) 3, 32
BC1409 BC1409 Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (NCBI ptt file) 3, 32
BC1410 BC1410 HisF protein (NCBI ptt file) 32, 344
BC1411 BC1411 Phosphoribosyl-AMP cyclohydrolase (NCBI ptt file) 3, 32
BC1412 BC1412 Phosphoribosyl-ATP pyrophosphatase (NCBI ptt file) 3, 32
BC1776 BC1776 Branched-chain amino acid aminotransferase (NCBI ptt file) 32, 297
BC1777 BC1777 Acetolactate synthase large subunit (NCBI ptt file) 32, 297
BC1779 BC1779 Ketol-acid reductoisomerase (NCBI ptt file) 32, 297
BC1780 BC1780 Dihydroxy-acid dehydratase (NCBI ptt file) 32, 297
BC1781 BC1781 Threonine dehydratase (NCBI ptt file) 32, 297
BC3167 BC3167 Xanthine dehydrogenase FAD-binding subunit (NCBI ptt file) 3, 347
BC3168 BC3168 Xanthine dehydrogenase molybdopterin-binding subunit (NCBI ptt file) 3, 347
BC3475 BC3475 hypothetical protein (NCBI ptt file) 3, 217
BC4699 BC4699 None 3, 83
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 BC0742
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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