Organism : Bacillus cereus ATCC14579 | Module List :
BC2770

Transcriptional regulator, DeoR family (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators of sugar metabolism cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2770
(Mouseover regulator name to see its description)

BC2770 is regulated by 24 influences and regulates 35 modules.
Regulators for BC2770 (24)
Regulator Module Operator
BC0595 496 tf
BC0680 496 tf
BC0785 496 tf
BC0854 496 tf
BC0953 496 tf
BC1080 496 tf
BC1337 496 tf
BC2386 496 tf
BC2558 496 tf
BC2672 496 tf
BC2770 496 tf
BC2996 496 tf
BC3062 496 tf
BC4010 496 tf
BC4960 496 tf
BC5173 496 tf
BC1080 409 tf
BC1296 409 tf
BC1915 409 tf
BC2738 409 tf
BC2770 409 tf
BC3826 409 tf
BC4072 409 tf
BC5352 409 tf

Warning: BC2770 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
4728 2.10e-01 GtagCGtaaGtAGactG
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4729 9.80e+01 catGAtaatgGtagGGagA
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4902 8.50e-03 tgaAaggaGGG
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4903 1.10e+04 GAaA.AaAgtgcTA
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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 BC2770

BC2770 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators of sugar metabolism cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC2770

BC2770 has total of 44 gene neighbors in modules 409, 496
Gene neighbors (44)
Gene Common Name Description Module membership
BC0419 BC0419 Hydroxyethylthiazole kinase (NCBI ptt file) 409, 491
BC0420 BC0420 Thiamin-phosphate pyrophosphorylase (NCBI ptt file) 409, 491
BC0552 BC0552 Internalin protein (NCBI ptt file) 358, 496
BC0686 BC0686 hypothetical protein (NCBI ptt file) 47, 409
BC0765 BC0765 hypothetical protein (NCBI ptt file) 496, 497
BC1018 BC1018 hypothetical protein (NCBI ptt file) 184, 496
BC1117 BC1117 hypothetical protein (NCBI ptt file) 184, 496
BC1146 BC1146 Stage 0 sporulation regulatory protein (NCBI ptt file) 26, 496
BC1348 BC1348 hypothetical protein (NCBI ptt file) 73, 409
BC1484 BC1484 ATP-dependent DNA helicase recQ (NCBI ptt file) 286, 409
BC1610 BC1610 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI ptt file) 409, 491
BC1773 BC1773 hypothetical protein (NCBI ptt file) 333, 496
BC1909 BC1909 XpaF1 protein (NCBI ptt file) 205, 496
BC1927 BC1927 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein (NCBI ptt file) 409, 434
BC1933 BC1933 hypothetical protein (NCBI ptt file) 434, 496
BC2051 BC2051 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 29, 409
BC2053 BC2053 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 409, 420
BC2066 BC2066 Macrolide glycosyltransferase (NCBI ptt file) 48, 496
BC2113 BC2113 hypothetical protein (NCBI ptt file) 48, 496
BC2145 BC2145 5-methylcytosine-specific restriction enzyme A (NCBI ptt file) 299, 409
BC2403 BC2403 hypothetical protein (NCBI ptt file) 333, 496
BC2478 BC2478 ABC transporter ATP-binding protein (NCBI ptt file) 409, 491
BC2658 BC2658 Serine/threonine protein kinase (NCBI ptt file) 203, 409
BC2714 BC2714 Acetyltransferase (NCBI ptt file) 47, 409
BC2770 BC2770 Transcriptional regulator, DeoR family (NCBI ptt file) 409, 496
BC2786 BC2786 hypothetical protein (NCBI ptt file) 358, 496
BC2787 BC2787 HIT family hydrolase (NCBI ptt file) 434, 496
BC2852 BC2852 Cell division protein DIVIC (NCBI ptt file) 409, 491
BC2855 BC2855 Transcriptional regulator, AraC family (NCBI ptt file) 362, 496
BC2934 BC2934 hypothetical Cytosolic Protein (NCBI ptt file) 333, 496
BC3100 BC3100 Sporulation kinase (NCBI ptt file) 496, 497
BC3219 BC3219 hypothetical protein (NCBI ptt file) 333, 409
BC3220 BC3220 hypothetical protein (NCBI ptt file) 299, 409
BC3231 BC3231 Microcin C7 self-immunity protein mccF (NCBI ptt file) 279, 409
BC3263 BC3263 hypothetical Cytosolic Protein (NCBI ptt file) 299, 496
BC3450 BC3450 hypothetical Membrane Spanning Protein (NCBI ptt file) 358, 496
BC3451 BC3451 hypothetical Membrane Spanning Protein (NCBI ptt file) 454, 496
BC3632 BC3632 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 333, 496
BC3633 BC3633 hypothetical protein (NCBI ptt file) 333, 496
BC3672 BC3672 hypothetical protein (NCBI ptt file) 173, 409
BC4074 BC4074 Anti-sigma F factor antagonist (NCBI ptt file) 203, 409
BC4615 BC4615 hypothetical protein (NCBI ptt file) 496, 497
BC4616 BC4616 hypothetical protein (NCBI ptt file) 496, 497
BC5322 BC5322 Nitrilotriacetate monooxygenase component B (NCBI ptt file) 173, 409
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 BC2770
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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