Organism : Bacillus cereus ATCC14579 | Module List :
BC3832

Nucleotide-binding SMF protein (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake cog/ cog
DNA mediated transformation go/ biological_process
dprA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3832
(Mouseover regulator name to see its description)

BC3832 is regulated by 20 influences and regulates 0 modules.
Regulators for BC3832 (20)
Regulator Module Operator
BC0230 314 tf
BC1080 314 tf
BC1329 314 tf
BC2410 314 tf
BC2760 314 tf
BC2801 314 tf
BC3588 314 tf
BC3904 314 tf
BC4930 314 tf
BC5205 314 tf
BC0230 398 tf
BC0785 398 tf
BC1080 398 tf
BC1987 398 tf
BC2410 398 tf
BC2760 398 tf
BC2770 398 tf
BC4072 398 tf
BC4393 398 tf
BC4499 398 tf

Warning: BC3832 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
4542 9.10e-02 AtAgaaaGaGg
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4543 6.50e+02 AGgAGA
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4706 1.70e+00 aaaagGAGaTgagt
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4707 5.90e+03 GCGcTaaGCGGc
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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 BC3832

BC3832 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake cog/ cog
DNA mediated transformation go/ biological_process
dprA tigr/ tigrfam
Module neighborhood information for BC3832

BC3832 has total of 31 gene neighbors in modules 314, 398
Gene neighbors (31)
Gene Common Name Description Module membership
BC0230 BC0230 Transcriptional regulator, LacI family (NCBI ptt file) 314, 398
BC0573 BC0573 Two component system histidine kinase (NCBI ptt file) 113, 314
BC0614 BC0614 Small, acid-soluble spore protein (NCBI ptt file) 61, 314
BC0623 BC0623 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 314, 398
BC0713 BC0713 ATP-binding protein (P-loop) (NCBI ptt file) 309, 314
BC0785 BC0785 hypothetical protein (NCBI ptt file) 359, 398
BC0922 BC0922 hypothetical protein (NCBI ptt file) 56, 398
BC1380 BC1380 hypothetical protein (NCBI ptt file) 114, 314
BC1492 BC1492 hypothetical protein (NCBI ptt file) 336, 398
BC1696 BC1696 hypothetical protein (NCBI ptt file) 398, 497
BC1697 BC1697 Asparagine synthetase [glutamine-hydrolyzing] (NCBI ptt file) 398, 446
BC2140 BC2140 N-hydroxyarylamine O-acetyltransferase (NCBI ptt file) 398, 472
BC2278 BC2278 Short chain dehydrogenase (NCBI ptt file) 21, 398
BC2571 BC2571 hypothetical protein (NCBI ptt file) 330, 398
BC2669 BC2669 ThiJ/PfpI family protein (NCBI ptt file) 330, 398
BC2760 BC2760 Transcriptional regulator, TetR family (NCBI ptt file) 309, 314
BC2768 BC2768 hypothetical Cytosolic Protein (NCBI ptt file) 314, 336
BC2769 BC2769 Acetyltransferase (NCBI ptt file) 314, 336
BC2788 BC2788 hypothetical protein (NCBI ptt file) 102, 314
BC2801 BC2801 DNA topology modulation protein (NCBI ptt file) 68, 314
BC2968 BC2968 hypothetical protein (NCBI ptt file) 244, 398
BC3384 BC3384 Enhancin (NCBI ptt file) 21, 314
BC3464 BC3464 hypothetical protein (NCBI ptt file) 336, 398
BC3565 BC3565 Molybdopterin (MPT) converting factor, subunit 2 (NCBI ptt file) 153, 398
BC3568 BC3568 Formate transporter (NCBI ptt file) 398, 445
BC3744 BC3744 hypothetical protein (NCBI ptt file) 95, 314
BC3832 BC3832 Nucleotide-binding SMF protein (NCBI ptt file) 314, 398
BC4504 BC4504 Stress-responsive transcriptional regulator PspC (NCBI ptt file) 241, 398
BC4659 BC4659 Acetyl-coenzyme A synthetase (NCBI ptt file) 314, 336
BC4730 BC4730 Homoserine O-acetyltransferase (NCBI ptt file) 286, 398
BC5354 BC5354 ABC transporter permease protein (NCBI ptt file) 398, 469
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 BC3832
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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