Organism : Bacillus cereus ATCC14579 | Module List :
BC2848

Oligopeptide-binding protein oppA (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
ABC-type oligopeptide transport system, periplasmic component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
4-phytase activity go/ molecular_function
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2848
(Mouseover regulator name to see its description)

BC2848 is regulated by 30 influences and regulates 0 modules.
Regulators for BC2848 (30)
Regulator Module Operator
BC0224 356 tf
BC1282 356 tf
BC1818 356 tf
BC1884 356 tf
BC2517 356 tf
BC2903 356 tf
BC3588 356 tf
BC3704 356 tf
BC4001 356 tf
BC4222 356 tf
BC4256 356 tf
BC4672 356 tf
BC0057 154 tf
BC0410 154 tf
BC0601 154 tf
BC1080 154 tf
BC2362 154 tf
BC2526 154 tf
BC2670 154 tf
BC2738 154 tf
BC2801 154 tf
BC2811 154 tf
BC2979 154 tf
BC3434 154 tf
BC3589 154 tf
BC4072 154 tf
BC4101 154 tf
BC4165 154 tf
BC5205 154 tf
BC5409 154 tf

Warning: BC2848 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
4224 3.60e-02 AaaaAgGgGg
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4225 1.40e+04 GTGcGcaGcAGGTTC
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4622 1.30e+04 GgaaAAcg.aaa.A
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4623 3.80e-01 A.gaga.aGat.gGgaAgAa
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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 BC2848

BC2848 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
ABC-type oligopeptide transport system, periplasmic component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
4-phytase activity go/ molecular_function
ABC transporters kegg/ kegg pathway
Module neighborhood information for BC2848

BC2848 has total of 36 gene neighbors in modules 154, 356
Gene neighbors (36)
Gene Common Name Description Module membership
BC1012 BC1012 hypothetical protein (NCBI ptt file) 356, 464
BC1208 BC1208 Beta 1,4 glucosyltransferase (NCBI ptt file) 135, 356
BC1395 BC1395 hypothetical protein (NCBI ptt file) 154, 395
BC1797 BC1797 SAM-dependent methyltransferases (NCBI ptt file) 19, 356
BC1877 BC1877 Phage protein (NCBI ptt file) 342, 356
BC1880 BC1880 Phage protein (NCBI ptt file) 342, 356
BC1882 BC1882 Phage protein (NCBI ptt file) 244, 356
BC1883 BC1883 Phage protein (NCBI ptt file) 342, 356
BC1884 BC1884 Transcription state regulatory protein abrB (NCBI ptt file) 342, 356
BC1885 BC1885 Phage protein (NCBI ptt file) 342, 356
BC1886 BC1886 Phage protein (NCBI ptt file) 342, 356
BC1887 BC1887 Phage protein (NCBI ptt file) 342, 356
BC1888 BC1888 Phage protein (NCBI ptt file) 342, 356
BC2144 BC2144 5-methylcytosine-specific restriction enzyme A (NCBI ptt file) 34, 154
BC2253 BC2253 hypothetical Cytosolic Protein (NCBI ptt file) 85, 154
BC2331 BC2331 Inosine-uridine preferring nucleoside hydrolase (NCBI ptt file) 154, 238
BC2413 BC2413 Phage protein (NCBI ptt file) 150, 154
BC2602 BC2602 hypothetical protein (NCBI ptt file) 154, 407
BC2670 BC2670 Transcriptional regulator, DeoR family (NCBI ptt file) 154, 308
BC2781 BC2781 Probable short-chain type dehydrogenase/reductase vdlC (NCBI ptt file) 113, 154
BC2802 BC2802 IG hypothetical 16873 (NCBI ptt file) 113, 154
BC2804 BC2804 hypothetical Cytosolic Protein (NCBI ptt file) 47, 154
BC2848 BC2848 Oligopeptide-binding protein oppA (NCBI ptt file) 154, 356
BC2849 BC2849 Cell wall-associated hydrolase (NCBI ptt file) 178, 356
BC3051 BC3051 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 154, 395
BC3294 BC3294 hypothetical Cytosolic Protein (NCBI ptt file) 4, 356
BC3338 BC3338 hypothetical Membrane Spanning Protein (NCBI ptt file) 154, 395
BC3504 BC3504 (S)-2-hydroxy-acid oxidase chain D (NCBI ptt file) 154, 163
BC3585 BC3585 Oligopeptide-binding protein oppA (NCBI ptt file) 356, 418
BC3658 BC3658 hypothetical ATP-binding protein (NCBI ptt file) 154, 427
BC3660 BC3660 hypothetical protein (NCBI ptt file) 123, 154
BC3967 BC3967 hypothetical protein (NCBI ptt file) 154, 217
BC4034 BC4034 Nitrilase (NCBI ptt file) 23, 154
BC4101 BC4101 Transcriptional regulator, copG family (NCBI ptt file) 113, 154
BC4348 BC4348 Phosphoglycerate mutase family (NCBI ptt file) 114, 356
BC4641 BC4641 hypothetical protein (NCBI ptt file) 154, 217
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 BC2848
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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