Organism : Bacillus cereus ATCC14579 | Module List :
BC3823

Uridylate kinase (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
Uridylate kinase cog/ cog
pyrimidine nucleotide biosynthetic process go/ biological_process
cellular amino acid biosynthetic process go/ biological_process
uridylate kinase activity go/ molecular_function
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
pyrH_bact tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3823
(Mouseover regulator name to see its description)

BC3823 is regulated by 26 influences and regulates 0 modules.
Regulators for BC3823 (26)
Regulator Module Operator
BC0116 513 tf
BC0122 513 tf
BC0158 513 tf
BC0266 513 tf
BC3128 513 tf
BC3690 513 tf
BC3814 513 tf
BC3976 513 tf
BC4057 513 tf
BC4204 513 tf
BC4289 513 tf
BC4316 513 tf
BC4603 513 tf
BC4661 513 tf
BC5339 513 tf
BC0116 471 tf
BC0122 471 tf
BC0123 471 tf
BC0880 471 tf
BC1387 471 tf
BC3814 471 tf
BC4289 471 tf
BC4603 471 tf
BC4859 471 tf
BC5191 471 tf
BC5339 471 tf

Warning: BC3823 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
4852 2.80e+01 gAgAaGaAGgG
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4853 2.10e+03 GCCAcCACC
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4936 5.90e+00 GagatGGAa.g
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4937 7.20e+01 GTA.GACAgg
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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 BC3823

BC3823 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Uridylate kinase cog/ cog
pyrimidine nucleotide biosynthetic process go/ biological_process
cellular amino acid biosynthetic process go/ biological_process
uridylate kinase activity go/ molecular_function
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
pyrH_bact tigr/ tigrfam
Module neighborhood information for BC3823

BC3823 has total of 23 gene neighbors in modules 471, 513
Gene neighbors (23)
Gene Common Name Description Module membership
BC0054 BC0054 Glucosamine-1-phosphate acetyltransferase (NCBI ptt file) 447, 513
BC0055 BC0055 Ribose-phosphate pyrophosphokinase (NCBI ptt file) 471, 513
BC0084 BC0084 Lysyl-tRNA synthetase (NCBI ptt file) 326, 471
BC0108 BC0108 Glutamyl-tRNA synthetase (NCBI ptt file) 270, 471
BC1198 BC1198 GTP pyrophosphokinase (NCBI ptt file) 455, 513
BC1372 BC1372 D-alanine-activating enzyme (NCBI ptt file) 325, 513
BC1453 BC1453 Low-affinity inorganic phosphate transporter (NCBI ptt file) 269, 471
BC1546 BC1546 Aspartate aminotransferase (NCBI ptt file) 300, 471
BC3821 BC3821 Undecaprenyl pyrophosphate synthetase (NCBI ptt file) 366, 471
BC3822 BC3822 Ribosome Recycling Factor (RRF) (NCBI ptt file) 300, 471
BC3823 BC3823 Uridylate kinase (NCBI ptt file) 471, 513
BC3824 BC3824 Protein Translation Elongation Factor Ts (EF-Ts) (NCBI ptt file) 360, 471
BC3869 BC3869 Guanylate kinase (NCBI ptt file) 471, 513
BC3870 BC3870 hypothetical protein (NCBI ptt file) 145, 513
BC4048 BC4048 Phosphoenolpyruvate-protein phosphotransferase (NCBI ptt file) 188, 471
BC4270 BC4270 Penicillin-binding protein (NCBI ptt file) 94, 513
BC4599 BC4599 Pyruvate kinase (NCBI ptt file) 169, 471
BC4600 BC4600 6-phosphofructokinase (NCBI ptt file) 169, 513
BC4746 BC4746 Fe-S oxidoreductase (NCBI ptt file) 325, 513
BC4747 BC4747 SAM-dependent methyltransferase (NCBI ptt file) 325, 513
BC4853 BC4853 Naphthoate synthase (NCBI ptt file) 326, 471
BC5088 BC5088 putative lantibiotic precursor peptide (NCBI ptt file) 226, 513
BC5329 BC5329 Bacterial Peptide Chain Release Factor 1 (RF-1) (NCBI ptt file) 269, 471
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 BC3823
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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