Organism : Bacillus cereus ATCC14579 | Module List :
BC2672

Methyltransferase (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
methyltransferase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2672
(Mouseover regulator name to see its description)

BC2672 is regulated by 23 influences and regulates 39 modules.
Regulators for BC2672 (23)
Regulator Module Operator
BC0057 395 tf
BC0473 395 tf
BC1080 395 tf
BC1698 395 tf
BC1814 395 tf
BC2738 395 tf
BC3244 395 tf
BC3493 395 tf
BC3702 395 tf
BC3922 395 tf
BC4072 395 tf
BC5363 395 tf
BC0598 330 tf
BC1915 330 tf
BC2672 330 tf
BC2760 330 tf
BC2770 330 tf
BC2979 330 tf
BC3128 330 tf
BC3493 330 tf
BC4072 330 tf
BC4104 330 tf
BC5265 330 tf

Warning: BC2672 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
4574 1.30e+01 CaCCtccT
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4575 1.40e+04 CTTcCATGCcG
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4700 9.40e-07 aAAGggGg
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4701 3.10e+03 GTTGC.GCTGT
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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 BC2672

BC2672 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
methyltransferase activity go/ molecular_function
Module neighborhood information for BC2672

BC2672 has total of 40 gene neighbors in modules 330, 395
Gene neighbors (40)
Gene Common Name Description Module membership
BC0222 BC0222 Periplasmic molybdate-binding protein (NCBI ptt file) 85, 395
BC0345 BC0345 Isochorismatase (NCBI ptt file) 299, 395
BC0395 BC0395 Metal-dependent hydrolase (NCBI ptt file) 72, 330
BC0898 BC0898 3-hydroxybutyryl-CoA dehydratase (NCBI ptt file) 112, 395
BC1062 BC1062 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file) 34, 330
BC1071 BC1071 hypothetical protein (NCBI ptt file) 194, 330
BC1338 BC1338 Oligoendopeptidase F (NCBI ptt file) 203, 395
BC1347 BC1347 hypothetical protein (NCBI ptt file) 54, 330
BC1395 BC1395 hypothetical protein (NCBI ptt file) 154, 395
BC1396 BC1396 Branched-chain amino acid aminotransferase (NCBI ptt file) 137, 330
BC1567 BC1567 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 299, 395
BC1594 BC1594 Isochorismatase (NCBI ptt file) 203, 395
BC1604 BC1604 hypothetical protein (NCBI ptt file) 25, 330
BC1607 BC1607 Fatty acid hydroxylase FAH1P (NCBI ptt file) 163, 395
BC1748 BC1748 Aspartokinase (NCBI ptt file) 330, 397
BC2105 BC2105 Lactoylglutathione lyase (NCBI ptt file) 395, 413
BC2182 BC2182 Histidinol-phosphatase (NCBI ptt file) 203, 395
BC2183 BC2183 Acetyltransferase (NCBI ptt file) 203, 395
BC2475 BC2475 hypothetical Membrane Spanning Protein (NCBI ptt file) 395, 502
BC2511 BC2511 hypothetical protein (NCBI ptt file) 160, 395
BC2571 BC2571 hypothetical protein (NCBI ptt file) 330, 398
BC2669 BC2669 ThiJ/PfpI family protein (NCBI ptt file) 330, 398
BC2672 BC2672 Methyltransferase (NCBI ptt file) 330, 395
BC2706 BC2706 Acetyltransferase (NCBI ptt file) 230, 395
BC2708 BC2708 hypothetical Cytosolic Protein (NCBI ptt file) 279, 395
BC2803 BC2803 Ubiquinone/menaquinone biosynthesis methyltransferase UBIE (NCBI ptt file) 113, 395
BC3021 BC3021 hypothetical Cytosolic Protein (NCBI ptt file) 112, 395
BC3034 BC3034 Cytosine deaminase (NCBI ptt file) 113, 395
BC3036 BC3036 hypothetical protein (NCBI ptt file) 395, 469
BC3051 BC3051 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 154, 395
BC3338 BC3338 hypothetical Membrane Spanning Protein (NCBI ptt file) 154, 395
BC3455 BC3455 Amino acid permease (NCBI ptt file) 330, 488
BC3519 BC3519 Response regulator aspartate phosphatase inhibitor (NCBI ptt file) 330, 395
BC3556 BC3556 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file) 395, 413
BC3580 BC3580 hypothetical protein (NCBI ptt file) 330, 488
BC3590 BC3590 ABC transporter permease protein (NCBI ptt file) 330, 427
BC3591 BC3591 ABC transporter ATP-binding protein (NCBI ptt file) 330, 427
BC3954 BC3954 hypothetical protein (NCBI ptt file) 330, 375
BC4515 BC4515 Esterase (NCBI ptt file) 330, 488
BC4946 BC4946 hypothetical protein (NCBI ptt file) 63, 330
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 BC2672
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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