Organism : Bacillus cereus ATCC14579 | Module List :
BC4968

Transcriptional activator tipA (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4968
(Mouseover regulator name to see its description)

BC4968 is regulated by 21 influences and regulates 10 modules.
Regulators for BC4968 (21)
Regulator Module Operator
BC1083 495 tf
BC1335 495 tf
BC1680 495 tf
BC1756 495 tf
BC2401 495 tf
BC2469 495 tf
BC2517 495 tf
BC2964 495 tf
BC4474 495 tf
BC4930 495 tf
BC4968 495 tf
BC0230 446 tf
BC1134 446 tf
BC1329 446 tf
BC2469 446 tf
BC2964 446 tf
BC3062 446 tf
BC4474 446 tf
BC4834 446 tf
BC4968 446 tf
BC5251 446 tf

Warning: BC4968 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
4802 7.00e-01 gacctt.tCaCtttTtcctat
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4803 8.70e+03 CGCcCG
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4900 2.20e-05 tttGgaggga.aGAg
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4901 2.50e+03 GGGCGcTG
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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 BC4968

BC4968 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC4968

BC4968 has total of 33 gene neighbors in modules 446, 495
Gene neighbors (33)
Gene Common Name Description Module membership
BC0619 BC0619 Iron(III) dicitrate transport ATP-binding protein fecE (NCBI ptt file) 54, 446
BC0633 BC0633 Spore germination protein KC (NCBI ptt file) 189, 446
BC0822 BC0822 CotJB protein (NCBI ptt file) 291, 495
BC0825 BC0825 hypothetical protein (NCBI ptt file) 250, 446
BC0984 BC0984 DNA-binding protein (NCBI ptt file) 224, 446
BC1017 BC1017 hypothetical protein (NCBI ptt file) 158, 446
BC1122 BC1122 hypothetical protein (NCBI ptt file) 327, 446
BC1529 BC1529 DNA polymerase, bacteriophage-type (NCBI ptt file) 407, 446
BC1697 BC1697 Asparagine synthetase [glutamine-hydrolyzing] (NCBI ptt file) 398, 446
BC1747 BC1747 Glyoxalase family protein (NCBI ptt file) 220, 446
BC1749 BC1749 hypothetical protein (NCBI ptt file) 405, 495
BC1751 BC1751 hypothetical protein (NCBI ptt file) 405, 495
BC1753 BC1753 Tetracycline resistance determinant tetV (NCBI ptt file) 125, 495
BC1917 BC1917 Phage protein (NCBI ptt file) 495, 519
BC2245 BC2245 6-acetamido-3-oxohexanoate aminotransferase (NCBI ptt file) 362, 495
BC2248 BC2248 Acetylornithine deacetylase (NCBI ptt file) 362, 495
BC2596 BC2596 Phage endopeptidase (NCBI ptt file) 153, 446
BC2789 BC2789 hypothetical protein (NCBI ptt file) 405, 495
BC2850 BC2850 Mandelate racemase/muconate lactonizing enzyme family protein (NCBI ptt file) 358, 446
BC2864 BC2864 Two-component response regulator (NCBI ptt file) 102, 495
BC3017 BC3017 hypothetical Secreted Protein (NCBI ptt file) 327, 446
BC3187 BC3187 Penicillin-binding protein (NCBI ptt file) 384, 495
BC3422 BC3422 hypothetical protein (NCBI ptt file) 446, 495
BC3552 BC3552 Inosine-uridine preferring nucleoside hydrolase (NCBI ptt file) 446, 495
BC3627 BC3627 Acetyl-CoA acetyltransferase (NCBI ptt file) 384, 495
BC3629 BC3629 BioY protein (NCBI ptt file) 111, 495
BC4060 BC4060 RibT protein (NCBI ptt file) 197, 446
BC4778 BC4778 ABC transporter substrate-binding protein (NCBI ptt file) 378, 495
BC4779 BC4779 ABC transporter ATP-binding protein (NCBI ptt file) 123, 495
BC4833 BC4833 hypothetical Membrane Spanning Protein (NCBI ptt file) 446, 495
BC4834 BC4834 Transcriptional regulator, ArsR family (NCBI ptt file) 89, 446
BC4968 BC4968 Transcriptional activator tipA (NCBI ptt file) 446, 495
BC5210 BC5210 PTS system, lichenan oligosaccharide-specific IIA component (NCBI ptt file) 212, 446
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 BC4968
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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