Organism : Bacillus cereus ATCC14579 | Module List :
BC0975

Transcriptional regulator, MarR family (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators 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 BC0975
(Mouseover regulator name to see its description)

BC0975 is regulated by 15 influences and regulates 10 modules.
Regulators for BC0975 (15)
Regulator Module Operator
BC0433 386 tf
BC0975 386 tf
BC1131 386 tf
BC1756 386 tf
BC1814 386 tf
BC5361 386 tf
BC5363 386 tf
BC0433 315 tf
BC0975 315 tf
BC1113 315 tf
BC1114 315 tf
BC1756 315 tf
BC2122 315 tf
BC5361 315 tf
BC5363 315 tf

Warning: BC0975 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
4544 4.20e+01 AAGggAGG
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4545 2.50e+02 TtcattAtaaaAgA.gACgaaaT
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4682 5.30e+02 aAGgtagg
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4683 5.70e+03 GTGGGG
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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 BC0975

BC0975 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators 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 BC0975

BC0975 has total of 24 gene neighbors in modules 315, 386
Gene neighbors (24)
Gene Common Name Description Module membership
BC0433 BC0433 Transcriptional regulator, TetR family (NCBI ptt file) 315, 386
BC0434 BC0434 Macrolide-efflux protein (NCBI ptt file) 315, 386
BC0975 BC0975 Transcriptional regulator, MarR family (NCBI ptt file) 315, 386
BC0976 BC0976 CDP-diacylglycerol--serine O-phosphatidyltransferase (NCBI ptt file) 315, 386
BC0977 BC0977 ATP synthase protein I (NCBI ptt file) 315, 386
BC0978 BC0978 Teicoplanin resistance protein vanZ (NCBI ptt file) 315, 386
BC1055 BC1055 hypothetical Membrane Spanning Protein (NCBI ptt file) 315, 369
BC1056 BC1056 hypothetical Membrane Spanning Protein (NCBI ptt file) 315, 369
BC1057 BC1057 hypothetical protein (NCBI ptt file) 315, 369
BC1113 BC1113 Sigma-M negative effector (NCBI ptt file) 315, 375
BC1114 BC1114 RNA polymerase sigma factor sigM (NCBI ptt file) 315, 386
BC1756 BC1756 Transcriptional repressor PadR (NCBI ptt file) 315, 386
BC1757 BC1757 Multidrug resistance protein B (NCBI ptt file) 315, 386
BC1812 BC1812 Aminopeptidase (NCBI ptt file) 315, 386
BC1813 BC1813 Carboxylic ester hydrolase (NCBI ptt file) 315, 386
BC1814 BC1814 Transcriptional regulator, TetR family (NCBI ptt file) 329, 386
BC1815 BC1815 Acetyltransferase (NCBI ptt file) 315, 386
BC2935 BC2935 None 315, 386
BC3218 BC3218 Penicillin-binding protein (NCBI ptt file) 315, 386
BC4140 BC4140 Mg(2+) transport ATPase, P-type (NCBI ptt file) 315, 386
BC4141 BC4141 Mg(2+) transport ATPase protein C (NCBI ptt file) 315, 386
BC5361 BC5361 ECF-type sigma factor negative effector (NCBI ptt file) 315, 386
BC5362 BC5362 ECF-type sigma factor negative effector (NCBI ptt file) 315, 386
BC5363 BC5363 RNA polymerase ECF-type sigma factor (NCBI ptt file) 315, 386
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 BC0975
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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