Organism : Bacillus cereus ATCC14579 | Module List :
BC2758

Metal-dependent hydrolase (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Predicted metal-dependent hydrolase cog/ cog
arylformamidase activity go/ molecular_function
trp_arylform tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2758
(Mouseover regulator name to see its description)

BC2758 is regulated by 28 influences and regulates 0 modules.
Regulators for BC2758 (28)
Regulator Module Operator
BC0114 137 tf
BC0598 137 tf
BC0613 137 tf
BC0856 137 tf
BC0954 137 tf
BC1622 137 tf
BC1841 137 tf
BC2362 137 tf
BC2632 137 tf
BC3493 137 tf
BC3826 137 tf
BC4057 137 tf
BC0224 258 tf
BC0356 258 tf
BC0473 258 tf
BC0607 258 tf
BC0993 258 tf
BC1427 258 tf
BC1531 258 tf
BC1724 258 tf
BC2217 258 tf
BC2770 258 tf
BC2971 258 tf
BC3072 258 tf
BC3493 258 tf
BC3922 258 tf
BC4072 258 tf
BC4525 258 tf

Warning: BC2758 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
4190 1.10e-11 tAGggGgaacaa
Loader icon
4191 2.80e-04 atAtgttAgAAtatTtAGAaaA
Loader icon
4432 5.20e-06 aaaGGgGa
Loader icon
4433 8.40e+03 GcCAaaAAGctaGGGtGcCG
Loader icon
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 BC2758

BC2758 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Predicted metal-dependent hydrolase cog/ cog
arylformamidase activity go/ molecular_function
trp_arylform tigr/ tigrfam
Module neighborhood information for BC2758

BC2758 has total of 53 gene neighbors in modules 137, 258
Gene neighbors (53)
Gene Common Name Description Module membership
BC0012 BC0012 IG hypothetical 16768 (NCBI ptt file) 137, 225
BC0013 BC0013 Inosine-5'-monophosphate dehydrogenase (NCBI ptt file) 63, 137
BC0114 BC0114 RNA polymerase sigma-H factor (NCBI ptt file) 137, 405
BC0215 BC0215 Oligopeptide-binding protein oppA (NCBI ptt file) 137, 408
BC0441 BC0441 Glucokinase (NCBI ptt file) 258, 362
BC0450 BC0450 Protein tyrosine phosphatase (NCBI ptt file) 112, 258
BC0451 BC0451 hypothetical protein (NCBI ptt file) 112, 258
BC0473 BC0473 Arginine utilization regulatory protein rocR (NCBI ptt file) 258, 375
BC0859 BC0859 Oligopeptide-binding protein oppA (NCBI ptt file) 137, 139
BC1149 BC1149 Ornithine aminotransferase (NCBI ptt file) 137, 488
BC1180 BC1180 Oligopeptide transport system permease protein oppB (NCBI ptt file) 23, 137
BC1181 BC1181 Oligopeptide transport system permease protein oppC (NCBI ptt file) 137, 434
BC1182 BC1182 Oligopeptide transport ATP-binding protein oppD (NCBI ptt file) 137, 358
BC1183 BC1183 Oligopeptide transport ATP-binding protein oppF (NCBI ptt file) 137, 434
BC1366 BC1366 SSEB protein (NCBI ptt file) 137, 284
BC1396 BC1396 Branched-chain amino acid aminotransferase (NCBI ptt file) 137, 330
BC1655 BC1655 hypothetical protein (NCBI ptt file) 258, 491
BC1785 BC1785 Acetyltransferase (NCBI ptt file) 258, 427
BC1799 BC1799 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 34, 137
BC1828 BC1828 Xaa-Pro aminopeptidase (NCBI ptt file) 194, 258
BC1912 BC1912 Phage protein (NCBI ptt file) 63, 137
BC1913 BC1913 Phage protein (NCBI ptt file) 63, 137
BC2094 BC2094 Acetyltransferase (NCBI ptt file) 137, 139
BC2142 BC2142 Stage V sporulation protein S (NCBI ptt file) 34, 137
BC2197 BC2197 Sec-independent protein translocase protein tatA (NCBI ptt file) 120, 258
BC2240 BC2240 Magnesium and cobalt efflux protein corC (NCBI ptt file) 163, 258
BC2757 BC2757 Tryptophan 2,3-dioxygenase (NCBI ptt file) 137, 218
BC2758 BC2758 Metal-dependent hydrolase (NCBI ptt file) 137, 258
BC2759 BC2759 L-kynurenine hydrolase (NCBI ptt file) 137, 218
BC2807 BC2807 hypothetical protein (NCBI ptt file) 47, 258
BC2808 BC2808 hypothetical Membrane Spanning Protein (NCBI ptt file) 47, 258
BC2809 BC2809 Phosphinothricin N-acetyltransferase (NCBI ptt file) 20, 258
BC2991 BC2991 Uridine kinase (NCBI ptt file) 258, 420
BC2992 BC2992 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 258, 420
BC3020 BC3020 hypothetical protein (NCBI ptt file) 163, 258
BC3157 BC3157 IG hypothetical 18565 (NCBI ptt file) 112, 258
BC3326 BC3326 hypothetical protein (NCBI ptt file) 258, 375
BC3415 BC3415 hypothetical protein (NCBI ptt file) 258, 375
BC3416 BC3416 SMS protein (NCBI ptt file) 105, 258
BC3418 BC3418 Phenazine biosynthesis protein phzF (NCBI ptt file) 258, 375
BC3494 BC3494 hypothetical protein (NCBI ptt file) 46, 137
BC3787 BC3787 Zinc protease (NCBI ptt file) 105, 258
BC3955 BC3955 hypothetical protein (NCBI ptt file) 137, 488
BC3968 BC3968 hypothetical protein (NCBI ptt file) 137, 491
BC4133 BC4133 Zinc metallohydrolase (NCBI ptt file) 137, 194
BC4427 BC4427 Prephenate dehydratase (NCBI ptt file) 73, 137
BC4682 BC4682 IAA acetyltransferase (NCBI ptt file) 137, 175
BC4683 BC4683 Ribosomal-protein-serine acetyltransferase (NCBI ptt file) 137, 175
BC4724 BC4724 Molybdenum cofactor biosynthesis protein A (NCBI ptt file) 237, 258
BC4950 BC4950 Nucleotidyltransferase (NCBI ptt file) 258, 375
BC5076 BC5076 Short chain dehydrogenase (NCBI ptt file) 73, 137
BC5077 BC5077 hypothetical protein (NCBI ptt file) 73, 137
BC5453 BC5453 Oligoendopeptidase F (NCBI ptt file) 137, 258
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 BC2758
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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