Organism : Bacillus cereus ATCC14579 | Module List :
BC3335

Protein tyrosine phosphatase (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Protein tyrosine/serine phosphatase cog/ cog
prenylated protein tyrosine phosphatase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3335
(Mouseover regulator name to see its description)

BC3335 is regulated by 31 influences and regulates 0 modules.
Regulators for BC3335 (31)
Regulator Module Operator
BC0059 382 tf
BC0099 382 tf
BC0116 382 tf
BC0122 382 tf
BC0595 382 tf
BC0657 382 tf
BC0993 382 tf
BC1337 382 tf
BC1363 382 tf
BC2122 382 tf
BC2979 382 tf
BC3826 382 tf
BC3868 382 tf
BC4240 382 tf
BC5332 382 tf
BC5402 382 tf
BC0116 148 tf
BC0595 148 tf
BC1033 148 tf
BC1363 148 tf
BC1889 148 tf
BC2401 148 tf
BC3982 148 tf
BC4010 148 tf
BC4057 148 tf
BC4081 148 tf
BC4204 148 tf
BC4356 148 tf
BC5200 148 tf
BC5339 148 tf
BC5368 148 tf

Warning: BC3335 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
4212 1.60e+01 atAtaAaAAtaaGa..G
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4213 6.50e+03 AggAaGgg
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4674 4.40e+00 GaAAGgGg
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4675 1.60e+04 AaAGaAGGtGaAA
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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 BC3335

BC3335 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Protein tyrosine/serine phosphatase cog/ cog
prenylated protein tyrosine phosphatase activity go/ molecular_function
Module neighborhood information for BC3335

BC3335 has total of 31 gene neighbors in modules 148, 382
Gene neighbors (31)
Gene Common Name Description Module membership
BC0363 BC0363 Nucleoside permease nupC (NCBI ptt file) 234, 382
BC0470 BC0470 S-layer protein / N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 382, 481
BC0542 BC0542 Thiol-disulfide oxidoreductase BdbD (NCBI ptt file) 37, 382
BC0682 BC0682 Sortase (NCBI ptt file) 148, 442
BC0685 BC0685 Branched-chain amino acid transport system carrier protein (NCBI ptt file) 134, 382
BC0689 BC0689 Guanine-hypoxanthine permease (NCBI ptt file) 6, 148
BC0888 BC0888 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 214, 382
BC1033 BC1033 Glycerol uptake operon antiterminator regulatory protein (NCBI ptt file) 37, 148
BC1070 BC1070 Protoporphyrinogen oxidase (NCBI ptt file) 311, 382
BC1074 BC1074 hypothetical protein (NCBI ptt file) 148, 440
BC1277 BC1277 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 148, 482
BC1384 BC1384 Bacitracin resistance protein (Putative undecaprenol kinase) (NCBI ptt file) 382, 481
BC1496 BC1496 L-asparaginase (NCBI ptt file) 290, 382
BC2096 BC2096 hypothetical protein (NCBI ptt file) 148, 260
BC2418 BC2418 hypothetical protein (NCBI ptt file) 148, 442
BC2703 BC2703 hypothetical protein (NCBI ptt file) 97, 148
BC2755 BC2755 Integral membrane protein (NCBI ptt file) 10, 148
BC2818 BC2818 hypothetical Cytosolic Protein (NCBI ptt file) 148, 249
BC2929 BC2929 Peptidoglycan N-acetylglucosamine deacetylase (NCBI ptt file) 382, 399
BC2977 BC2977 Pyrroline-5-carboxylate reductase (NCBI ptt file) 148, 249
BC3335 BC3335 Protein tyrosine phosphatase (NCBI ptt file) 148, 382
BC3765 BC3765 Phosphoglycerol transferase (NCBI ptt file) 133, 382
BC3912 BC3912 UDP-N-acetylmuramoylalanine--D-glutamate ligase (NCBI ptt file) 283, 382
BC3956 BC3956 GTP-binding protein TypA/BipA (NCBI ptt file) 382, 477
BC3975 BC3975 hydrolase (HAD superfamily) (NCBI ptt file) 148, 442
BC4020 BC4020 hypothetical protein (NCBI ptt file) 148, 442
BC4024 BC4024 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 341, 382
BC4356 BC4356 Transcriptional regulator, MerR family (NCBI ptt file) 55, 148
BC4942 BC4942 PhnA protein (NCBI ptt file) 62, 382
BC5337 BC5337 hypothetical protein (NCBI ptt file) 148, 249
BC5370 BC5370 Agmatinase (NCBI ptt file) 257, 382
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 BC3335
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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