Organism : Bacillus cereus ATCC14579 | Module List :
BC1548

Endonuclease III (NCBI ptt file)

CircVis
Functional Annotations (10)
Function System
Predicted EndoIII-related endonuclease cog/ cog
DNA-(apurinic or apyrimidinic site) lyase activity go/ molecular_function
endonuclease activity go/ molecular_function
iron ion binding go/ molecular_function
intracellular go/ cellular_component
base-excision repair go/ biological_process
sequence-specific DNA binding go/ molecular_function
4 iron, 4 sulfur cluster binding go/ molecular_function
Base excision repair kegg/ kegg pathway
nth tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1548
(Mouseover regulator name to see its description)

BC1548 is regulated by 23 influences and regulates 0 modules.
Regulators for BC1548 (23)
Regulator Module Operator
BC0116 269 tf
BC1282 269 tf
BC3813 269 tf
BC3814 269 tf
BC4170 269 tf
BC4212 269 tf
BC4289 269 tf
BC4316 269 tf
BC5332 269 tf
BC5339 269 tf
BC0116 142 tf
BC3706 142 tf
BC3814 142 tf
BC3891 142 tf
BC3922 142 tf
BC4170 142 tf
BC4206 142 tf
BC4212 142 tf
BC4499 142 tf
BC5205 142 tf
BC5265 142 tf
BC5332 142 tf
BC5339 142 tf

Warning: BC1548 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
4200 2.60e+02 CCTCCc
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4201 2.20e+03 AAaAAgAaAta.gc
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4454 1.30e+03 aCTCCC
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4455 5.20e+03 .GtGgtGg
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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 BC1548

BC1548 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Predicted EndoIII-related endonuclease cog/ cog
DNA-(apurinic or apyrimidinic site) lyase activity go/ molecular_function
endonuclease activity go/ molecular_function
iron ion binding go/ molecular_function
intracellular go/ cellular_component
base-excision repair go/ biological_process
sequence-specific DNA binding go/ molecular_function
4 iron, 4 sulfur cluster binding go/ molecular_function
Base excision repair kegg/ kegg pathway
nth tigr/ tigrfam
Module neighborhood information for BC1548

BC1548 has total of 25 gene neighbors in modules 142, 269
Gene neighbors (25)
Gene Common Name Description Module membership
BC0232 BC0232 hypothetical Membrane Spanning Protein (NCBI ptt file) 142, 300
BC1453 BC1453 Low-affinity inorganic phosphate transporter (NCBI ptt file) 269, 471
BC1454 BC1454 putative pit accessory protein (NCBI ptt file) 14, 269
BC1547 BC1547 DNA replication protein dnaD (NCBI ptt file) 269, 372
BC1548 BC1548 Endonuclease III (NCBI ptt file) 142, 269
BC1549 BC1549 hypothetical protein (NCBI ptt file) 142, 269
BC3604 BC3604 hypothetical Membrane Spanning Protein (NCBI ptt file) 142, 396
BC3705 BC3705 None 133, 142
BC3706 BC3706 Transcriptional regulator, MerR family (NCBI ptt file) 133, 142
BC3836 BC3836 GTP-binding protein (NCBI ptt file) 269, 366
BC3871 BC3871 Protein yicC (NCBI ptt file) 142, 275
BC3922 BC3922 Prespore specific transcriptional activator rsfA (NCBI ptt file) 92, 142
BC4183 BC4183 Biotin carboxylase (NCBI ptt file) 269, 372
BC4289 BC4289 RNA polymerase sigma factor rpoD (NCBI ptt file) 269, 326
BC4308 BC4308 Fe-S oxidoreductase (NCBI ptt file) 94, 269
BC4317 BC4317 GTP-binding protein lepA (NCBI ptt file) 231, 269
BC5205 BC5205 Transcriptional regulatory protein levR (NCBI ptt file) 142, 304
BC5329 BC5329 Bacterial Peptide Chain Release Factor 1 (RF-1) (NCBI ptt file) 269, 471
BC5330 BC5330 Thymidine kinase (NCBI ptt file) 133, 142
BC5332 BC5332 Transcription termination factor rho (NCBI ptt file) 269, 372
BC5449 BC5449 Conserved membrane protein (hemolysin III homolog) (NCBI ptt file) 88, 142
BC5477 BC5477 GTP-binding protein (NCBI ptt file) 231, 269
BC5487 BC5487 Jag protein (NCBI ptt file) 142, 396
BC5488 BC5488 60 kDa inner membrane protein YIDC (NCBI ptt file) 269, 372
BC5489 BC5489 Ribonuclease P protein component (NCBI ptt file) 142, 161
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 BC1548
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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