Organism : Bacillus cereus ATCC14579 | Module List :
BC4960

Transcriptional regulator, DeoR family (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Predicted transcriptional regulator 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 BC4960
(Mouseover regulator name to see its description)

BC4960 is regulated by 16 influences and regulates 12 modules.
Regulators for BC4960 (16)
Regulator Module Operator
BC1851 334 tf
BC2680 334 tf
BC2837 334 tf
BC2964 334 tf
BC3653 334 tf
BC0518 30 tf
BC1253 30 tf
BC2362 30 tf
BC2526 30 tf
BC2904 30 tf
BC3449 30 tf
BC3700 30 tf
BC4211 30 tf
BC4314 30 tf
BC4661 30 tf
BC4960 30 tf

Warning: BC4960 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
3982 3.40e+02 AA.GgaGgaGaGtg
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3983 2.50e+04 GGTcCcCaTCG
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4580 1.70e-04 T.CCcCctTcattaT
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4581 6.70e+02 aaaGGaGG
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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 BC4960

BC4960 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted transcriptional regulator 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 BC4960

BC4960 has total of 66 gene neighbors in modules 30, 334
Gene neighbors (66)
Gene Common Name Description Module membership
BC0399 BC0399 Oxidoreductase (NCBI ptt file) 30, 85
BC0823 BC0823 CotJA protein (NCBI ptt file) 26, 334
BC0878 BC0878 IG hypothetical 16724 (NCBI ptt file) 17, 334
BC0904 BC0904 hypothetical protein (NCBI ptt file) 17, 334
BC1047 BC1047 Protease production regulatory protein hpr (NCBI ptt file) 30, 199
BC1065 BC1065 hypothetical Membrane Spanning Protein (NCBI ptt file) 30, 453
BC1429 BC1429 hypothetical protein (NCBI ptt file) 128, 334
BC1573 BC1573 hypothetical protein (NCBI ptt file) 186, 334
BC1625 BC1625 Chemotaxis motA protein (NCBI ptt file) 30, 199
BC1626 BC1626 Chemotaxis motB protein (NCBI ptt file) 30, 199
BC1656 BC1656 Flagellin (NCBI ptt file) 30, 85
BC1708 BC1708 hypothetical protein (NCBI ptt file) 30, 130
BC1723 BC1723 Prolipoprotein diacylglyceryl transferase (NCBI ptt file) 30, 250
BC1758 BC1758 hypothetical Membrane Spanning Protein (NCBI ptt file) 30, 147
BC1805 BC1805 hypothetical protein (NCBI ptt file) 186, 334
BC1808 BC1808 hypothetical protein (NCBI ptt file) 186, 334
BC1894 BC1894 Phage protein (NCBI ptt file) 272, 334
BC1905 BC1905 Phage protein (NCBI ptt file) 232, 334
BC1911 BC1911 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 205, 334
BC1928 BC1928 Branched-chain amino acid transport ATP-binding protein livG (NCBI ptt file) 334, 520
BC2007 BC2007 hypothetical protein (NCBI ptt file) 186, 334
BC2010 BC2010 hypothetical Membrane Spanning Protein (NCBI ptt file) 334, 463
BC2080 BC2080 hypothetical Membrane Associated Protein (NCBI ptt file) 30, 502
BC2081 BC2081 DNA segregation ATPase and related proteins (FtsK/SpoIIIE family) (NCBI ptt file) 30, 502
BC2085 BC2085 hypothetical protein (NCBI ptt file) 30, 502
BC2091 BC2091 hypothetical protein (NCBI ptt file) 186, 334
BC2149 BC2149 hypothetical protein (NCBI ptt file) 334, 417
BC2362 BC2362 Transcriptional regulators, LysR family (NCBI ptt file) 30, 85
BC2383 BC2383 Oxalate decarboxylase (NCBI ptt file) 272, 334
BC2509 BC2509 Sortase (NCBI ptt file) 17, 334
BC2526 BC2526 Transcriptional regulator, GntR family (NCBI ptt file) 30, 428
BC2712 BC2712 hypothetical protein (NCBI ptt file) 186, 334
BC2753 BC2753 Cell wall hydrolase cwlJ (NCBI ptt file) 334, 459
BC2875 BC2875 hypothetical protein (NCBI ptt file) 334, 339
BC2876 BC2876 Acetyltransferase (NCBI ptt file) 30, 364
BC2901 BC2901 ABC transporter permease protein (NCBI ptt file) 30, 204
BC2904 BC2904 Transcriptional regulator, GntR family (NCBI ptt file) 30, 60
BC2962 BC2962 Sugar transport system permease protein (NCBI ptt file) 199, 334
BC2981 BC2981 hypothetical protein (NCBI ptt file) 146, 334
BC3113 BC3113 Two-component response regulator ycbB (NCBI ptt file) 30, 199
BC3214 BC3214 hypothetical protein (NCBI ptt file) 30, 489
BC3215 BC3215 hypothetical protein (NCBI ptt file) 30, 253
BC3261 BC3261 hypothetical protein (NCBI ptt file) 30, 279
BC3360 BC3360 Methyltransferase (NCBI ptt file) 17, 334
BC3397 BC3397 hypothetical protein (NCBI ptt file) 186, 334
BC3510 BC3510 hypothetical protein (NCBI ptt file) 30, 291
BC3598 BC3598 hypothetical protein (NCBI ptt file) 186, 334
BC3618 BC3618 Peptidoglycan N-acetylglucosamine deacetylase (NCBI ptt file) 30, 517
BC3694 BC3694 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 30, 279
BC3695 BC3695 holin (NCBI ptt file) 30, 279
BC3698 BC3698 Cell wall endopeptidase, family M23/M37 (NCBI ptt file) 30, 279
BC3699 BC3699 Antigen (NCBI ptt file) 30, 279
BC3700 BC3700 Phage protein (NCBI ptt file) 30, 197
BC3733 BC3733 hypothetical protein (NCBI ptt file) 334, 339
BC3751 BC3751 hypothetical protein (NCBI ptt file) 334, 339
BC4002 BC4002 hypothetical protein (NCBI ptt file) 225, 334
BC4070 BC4070 Stage V sporulation protein AA (NCBI ptt file) 131, 334
BC4171 BC4171 hypothetical protein (NCBI ptt file) 17, 334
BC4512 BC4512 Chemotaxis motB protein (NCBI ptt file) 30, 158
BC4591 BC4591 MaoC family protein (NCBI ptt file) 199, 334
BC4595 BC4595 hypothetical protein (NCBI ptt file) 186, 334
BC4619 BC4619 hypothetical protein (NCBI ptt file) 30, 316
BC4635 BC4635 hypothetical protein (NCBI ptt file) 128, 334
BC4661 BC4661 Acetoin utilization acuB protein (NCBI ptt file) 30, 516
BC4960 BC4960 Transcriptional regulator, DeoR family (NCBI ptt file) 30, 334
BC5134 BC5134 Inosine-uridine preferring nucleoside hydrolase (NCBI ptt file) 186, 334
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 BC4960
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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