Organism : Bacillus cereus ATCC14579 | Module List :
BC2338

Ribosomal-protein-alanine acetyltransferase (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
metabolic process go/ biological_process
ribosomal-protein-alanine N-acetyltransferase activity go/ molecular_function
ribosomal-protein-alanine N-acetyltransferase complex go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2338
(Mouseover regulator name to see its description)

BC2338 is regulated by 23 influences and regulates 0 modules.
Regulators for BC2338 (23)
Regulator Module Operator
BC0742 210 tf
BC1080 210 tf
BC2122 210 tf
BC2178 210 tf
BC2410 210 tf
BC2469 210 tf
BC2760 210 tf
BC3588 210 tf
BC3868 210 tf
BC4072 210 tf
BC5205 210 tf
BC1080 244 tf
BC1537 244 tf
BC2410 244 tf
BC2469 244 tf
BC2517 244 tf
BC2549 244 tf
BC2760 244 tf
BC2988 244 tf
BC5176 244 tf
BC5205 244 tf
BC5402 244 tf
BC5409 244 tf

Warning: BC2338 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
4336 4.90e+01 gAAAtAgagaG
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4337 4.30e+03 GGaGGGAAGG
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4404 3.00e+02 GaaaGGggaagaA
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4405 5.30e+03 GCGcaaCcATCcccaTAacCTcC
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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 BC2338

BC2338 is enriched for 3 functions in 2 categories.
Enrichment Table (3)
Function System
metabolic process go/ biological_process
ribosomal-protein-alanine N-acetyltransferase activity go/ molecular_function
ribosomal-protein-alanine N-acetyltransferase complex go/ cellular_component
Module neighborhood information for BC2338

BC2338 has total of 28 gene neighbors in modules 210, 244
Gene neighbors (28)
Gene Common Name Description Module membership
BC0184 BC0184 Glycerate kinase (NCBI ptt file) 59, 244
BC0799 BC0799 hypothetical Membrane Spanning Protein (NCBI ptt file) 244, 338
BC0866 BC0866 Glutamate racemase (NCBI ptt file) 229, 244
BC1080 BC1080 Transcriptional regulator (NCBI ptt file) 29, 210
BC1125 BC1125 S-layer homology domain (NCBI ptt file) 29, 210
BC1209 BC1209 O-antigen biosynthesis protein rfbC (NCBI ptt file) 229, 244
BC1399 BC1399 Ketol-acid reductoisomerase (NCBI ptt file) 32, 244
BC1403 BC1403 3-isopropylmalate dehydratase small subunit (NCBI ptt file) 32, 244
BC1521 BC1521 hypothetical Cytosolic Protein (NCBI ptt file) 23, 210
BC1583 BC1583 O-acetyl transferase (NCBI ptt file) 244, 370
BC1882 BC1882 Phage protein (NCBI ptt file) 244, 356
BC1963 BC1963 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 244, 522
BC2050 BC2050 Stage II sporulation protein P (NCBI ptt file) 101, 210
BC2052 BC2052 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 29, 210
BC2271 BC2271 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 244, 347
BC2338 BC2338 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 210, 244
BC2410 BC2410 Transcriptional regulator, TetR family (NCBI ptt file) 210, 336
BC2411 BC2411 Macrolide-efflux protein (NCBI ptt file) 210, 336
BC2519 BC2519 Lipase (NCBI ptt file) 29, 210
BC2550 BC2550 D-alanine--D-alanine ligase (NCBI ptt file) 244, 490
BC2662 BC2662 Division specific D,D-transpeptidase / Cell division protein ftsI (NCBI ptt file) 210, 336
BC2684 BC2684 Spermine/spermidine acetyltransferase (NCBI ptt file) 113, 210
BC2685 BC2685 CutA1 divalent ion tolerance protein (NCBI ptt file) 113, 210
BC2968 BC2968 hypothetical protein (NCBI ptt file) 244, 398
BC3030 BC3030 hypothetical protein (NCBI ptt file) 244, 378
BC3637 BC3637 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 244, 377
BC4358 BC4358 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 210, 336
BC4956 BC4956 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 210, 437
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 BC2338
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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