Organism : Bacillus cereus ATCC14579 | Module List :
BC4703

Transcriptional regulator, DeoR family (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
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 BC4703
(Mouseover regulator name to see its description)

BC4703 is regulated by 27 influences and regulates 32 modules.
Regulators for BC4703 (27)
Regulator Module Operator
BC0518 129 tf
BC0742 129 tf
BC1113 129 tf
BC1936 129 tf
BC2358 129 tf
BC2434 129 tf
BC3062 129 tf
BC3163 129 tf
BC3255 129 tf
BC3356 129 tf
BC3449 129 tf
BC3813 129 tf
BC3891 129 tf
BC4101 129 tf
BC4652 129 tf
BC4670 129 tf
BC4703 129 tf
BC0518 119 tf
BC1710 119 tf
BC1936 119 tf
BC2434 119 tf
BC4256 119 tf
BC4670 119 tf
BC4703 119 tf
BC4714 119 tf
BC5010 119 tf
BC5481 119 tf

Warning: BC4703 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
4154 1.20e+00 TaggagAGGAgaGat
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4155 4.20e+02 at.taTg.TataaTaaAc.tAaa
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4174 1.10e-01 atTCCTCc
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4175 6.10e+02 CACTTGatTAGTAaA
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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 BC4703

BC4703 is enriched for 3 functions in 2 categories.
Enrichment Table (3)
Function System
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 BC4703

BC4703 has total of 46 gene neighbors in modules 119, 129
Gene neighbors (46)
Gene Common Name Description Module membership
BC0246 BC0246 hydrolase (HAD superfamily) (NCBI ptt file) 107, 129
BC0291 BC0291 AT-rich DNA-binding protein (NCBI ptt file) 119, 187
BC0397 BC0397 hypothetical Cytosolic Protein (NCBI ptt file) 129, 216
BC0472 BC0472 hypothetical protein (NCBI ptt file) 28, 119
BC0792 BC0792 hypothetical Cytosolic Protein (NCBI ptt file) 74, 119
BC1024 BC1024 Glyoxalase family protein (NCBI ptt file) 129, 224
BC1025 BC1025 Glyoxalase family protein (NCBI ptt file) 129, 224
BC1188 BC1188 Arsenate reductase family protein (NCBI ptt file) 129, 166
BC1491 BC1491 NAD-specific glutamate dehydrogenase (NCBI ptt file) 129, 445
BC1602 BC1602 hypothetical Cytosolic Protein (NCBI ptt file) 129, 381
BC1936 BC1936 Transcriptional regulator, MarR family (NCBI ptt file) 70, 129
BC1937 BC1937 Luciferase-like monooxygenase (NCBI ptt file) 70, 129
BC2011 BC2011 Non-specific DNA-binding protein Dps / Iron-binding ferritin-like antioxidant protein / Ferroxidase (NCBI ptt file) 119, 129
BC2012 BC2012 hypothetical protein (NCBI ptt file) 119, 166
BC2199 BC2199 hypothetical protein (NCBI ptt file) 119, 438
BC2213 BC2213 Pyrazinamidase (NCBI ptt file) 119, 438
BC2844 BC2844 None 129, 380
BC3525 BC3525 hypothetical Cytosolic Protein (NCBI ptt file) 129, 381
BC3974 BC3974 Polypeptide deformylase (NCBI ptt file) 119, 129
BC4091 BC4091 Ferric uptake regulation protein (NCBI ptt file) 118, 119
BC4139 BC4139 hypothetical protein (NCBI ptt file) 28, 119
BC4145 BC4145 hypothetical protein (NCBI ptt file) 74, 119
BC4167 BC4167 Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) 129, 422
BC4625 BC4625 Universal stress protein family (NCBI ptt file) 129, 187
BC4636 BC4636 MutT/nudix family protein (NCBI ptt file) 119, 438
BC4670 BC4670 putative transcriptional regulator (NCBI ptt file) 107, 119
BC4678 BC4678 Aminopeptidase (NCBI ptt file) 107, 119
BC4702 BC4702 Xaa-His dipeptidase (NCBI ptt file) 74, 119
BC4703 BC4703 Transcriptional regulator, DeoR family (NCBI ptt file) 119, 129
BC4714 BC4714 CarD-like transcriptional regulator (NCBI ptt file) 1, 119
BC4754 BC4754 putative acetyltransferase/acyltransferase (NCBI ptt file) 129, 422
BC4757 BC4757 Molybdopterin-guanine dinucleotide biosynthesis protein A (NCBI ptt file) 74, 119
BC4758 BC4758 Molybdenum cofactor biosynthesis protein B (NCBI ptt file) 119, 273
BC4797 BC4797 hypothetical protein (NCBI ptt file) 119, 501
BC4801 BC4801 Phage shock protein A (NCBI ptt file) 119, 129
BC4900 BC4900 S1-type RNA-binding domain (NCBI ptt file) 129, 227
BC4935 BC4935 HESB protein (NCBI ptt file) 1, 119
BC4936 BC4936 Diaminopimelate epimerase (NCBI ptt file) 119, 273
BC4992 BC4992 Arsenate reductase family protein (NCBI ptt file) 119, 126
BC5016 BC5016 60 kDa inner membrane protein YIDC (NCBI ptt file) 70, 129
BC5017 BC5017 hypothetical protein (NCBI ptt file) 70, 129
BC5190 BC5190 Probable Sigma (54) modulation protein / SSU ribosomal protein S30P (NCBI ptt file) 129, 187
BC5197 BC5197 Transcriptional regulator, MarR family (NCBI ptt file) 1, 119
BC5374 BC5374 Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) 129, 187
BC5437 BC5437 hypothetical Membrane Spanning Protein (NCBI ptt file) 119, 438
BC5481 BC5481 Stage 0 sporulation protein J (NCBI ptt file) 28, 119
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 BC4703
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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