Organism : Bacillus cereus ATCC14579 | Module List :
BC1929

Branched-chain amino acid transport ATP-binding protein livF (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
ABC-type branched-chain amino acid transport systems, ATPase component cog/ cog
ATP binding go/ molecular_function
ATPase activity go/ molecular_function
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1929
(Mouseover regulator name to see its description)

BC1929 is regulated by 17 influences and regulates 0 modules.
Regulators for BC1929 (17)
Regulator Module Operator
BC0648 206 tf
BC0742 206 tf
BC1033 206 tf
BC1059 206 tf
BC1329 206 tf
BC1851 206 tf
BC2178 206 tf
BC2401 206 tf
BC2469 206 tf
BC2517 206 tf
BC2680 206 tf
BC2837 206 tf
BC2964 206 tf
BC3588 206 tf
BC3903 206 tf
BC2964 186 tf
BC3982 186 tf

Warning: BC1929 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
4288 5.80e-05 ttCC.ccTtC
Loader icon
4289 2.40e+00 aAGGAGg
Loader icon
4328 2.70e+03 GGAGGG
Loader icon
4329 6.70e+02 GGgGcgaC
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 BC1929

BC1929 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
ABC-type branched-chain amino acid transport systems, ATPase component cog/ cog
ATP binding go/ molecular_function
ATPase activity go/ molecular_function
ABC transporters kegg/ kegg pathway
Module neighborhood information for BC1929

BC1929 has total of 45 gene neighbors in modules 186, 206
Gene neighbors (45)
Gene Common Name Description Module membership
BC0581 BC0581 hypothetical protein (NCBI ptt file) 31, 186
BC1206 BC1206 Macrocin O-methyltransferase (NCBI ptt file) 186, 232
BC1218 BC1218 Spore coat protein Y (NCBI ptt file) 186, 378
BC1245 BC1245 hypothetical protein (NCBI ptt file) 186, 468
BC1401 BC1401 3-isopropylmalate dehydrogenase (NCBI ptt file) 206, 280
BC1445 BC1445 hypothetical protein (NCBI ptt file) 186, 272
BC1539 BC1539 hypothetical protein (NCBI ptt file) 186, 327
BC1573 BC1573 hypothetical protein (NCBI ptt file) 186, 334
BC1706 BC1706 hypothetical Membrane Spanning Protein (NCBI ptt file) 186, 355
BC1714 BC1714 hypothetical protein (NCBI ptt file) 186, 225
BC1805 BC1805 hypothetical protein (NCBI ptt file) 186, 334
BC1808 BC1808 hypothetical protein (NCBI ptt file) 186, 334
BC1851 BC1851 Transcriptional regulator (NCBI ptt file) 206, 327
BC1895 BC1895 Phage protein (NCBI ptt file) 186, 321
BC1901 BC1901 Phage protein (NCBI ptt file) 186, 232
BC1929 BC1929 Branched-chain amino acid transport ATP-binding protein livF (NCBI ptt file) 186, 206
BC1930 BC1930 Branched-chain amino acid transport system permease protein livH (NCBI ptt file) 206, 520
BC2007 BC2007 hypothetical protein (NCBI ptt file) 186, 334
BC2091 BC2091 hypothetical protein (NCBI ptt file) 186, 334
BC2098 BC2098 hypothetical protein (NCBI ptt file) 179, 186
BC2244 BC2244 hypothetical protein (NCBI ptt file) 158, 186
BC2282 BC2282 hypothetical protein (NCBI ptt file) 135, 186
BC2350 BC2350 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 84, 206
BC2647 BC2647 hypothetical protein (NCBI ptt file) 186, 459
BC2681 BC2681 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 206, 289
BC2712 BC2712 hypothetical protein (NCBI ptt file) 186, 334
BC2762 BC2762 hypothetical protein (NCBI ptt file) 46, 186
BC2965 BC2965 Sugar (pentulose and hexulose) kinases (NCBI ptt file) 186, 199
BC2994 BC2994 hypothetical protein (NCBI ptt file) 186, 521
BC3099 BC3099 Spore germination protein QA (NCBI ptt file) 186, 393
BC3145 BC3145 hypothetical protein (NCBI ptt file) 186, 250
BC3147 BC3147 hypothetical protein (NCBI ptt file) 186, 487
BC3172 BC3172 hypothetical protein (NCBI ptt file) 186, 338
BC3357 BC3357 hypothetical protein (NCBI ptt file) 186, 339
BC3397 BC3397 hypothetical protein (NCBI ptt file) 186, 334
BC3579 BC3579 hypothetical Membrane Spanning Protein (NCBI ptt file) 17, 186
BC3598 BC3598 hypothetical protein (NCBI ptt file) 186, 334
BC3652 BC3652 Histidine ammonia-lyase (NCBI ptt file) 186, 337
BC3750 BC3750 UDP-N-acetylglucosamine 4,6-dehydratase (NCBI ptt file) 17, 186
BC4595 BC4595 hypothetical protein (NCBI ptt file) 186, 334
BC4862 BC4862 Lipase (NCBI ptt file) 186, 414
BC4916 BC4916 hypothetical Cytosolic Protein (NCBI ptt file) 186, 397
BC5134 BC5134 Inosine-uridine preferring nucleoside hydrolase (NCBI ptt file) 186, 334
BC5247 BC5247 hypothetical protein (NCBI ptt file) 123, 186
BC5360 BC5360 hypothetical protein (NCBI ptt file) 89, 186
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 BC1929
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