Organism : Bacillus cereus ATCC14579 | Module List :
BC1683

Transcriptional regulators, LysR family (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1683
(Mouseover regulator name to see its description)

BC1683 is regulated by 20 influences and regulates 2 modules.
Regulators for BC1683 (20)
Regulator Module Operator
BC0047 393 tf
BC0566 393 tf
BC0742 393 tf
BC1329 393 tf
BC1683 393 tf
BC2068 393 tf
BC2469 393 tf
BC2964 393 tf
BC3904 393 tf
BC4240 393 tf
BC5010 393 tf
BC5402 393 tf
BC1059 469 tf
BC1537 469 tf
BC1698 469 tf
BC1724 469 tf
BC4433 469 tf
BC4672 469 tf
BC5176 469 tf
BC5402 469 tf

Warning: BC1683 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
4696 3.90e-01 gGaGggAga.g
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4697 3.00e+01 acCttCTTTta.T.T
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4848 1.10e-03 AGAAtgagggg
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4849 5.30e+01 ggcATAtagaa.GAaAGcAG
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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 BC1683

BC1683 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC1683

BC1683 has total of 38 gene neighbors in modules 393, 469
Gene neighbors (38)
Gene Common Name Description Module membership
BC0047 BC0047 Sporulation-specific protease YabG (NCBI ptt file) 217, 393
BC0741 BC0741 hypothetical protein (NCBI ptt file) 17, 393
BC0969 BC0969 hypothetical protein (NCBI ptt file) 289, 469
BC1327 BC1327 (2-aminoethyl)phosphonate--pyruvate transaminase (NCBI ptt file) 59, 469
BC1328 BC1328 Saccharopine dehydrogenase [NADP+, L-lysine forming] (NCBI ptt file) 469, 516
BC1393 BC1393 hypothetical protein (NCBI ptt file) 353, 393
BC1456 BC1456 hypothetical protein (NCBI ptt file) 46, 393
BC1683 BC1683 Transcriptional regulators, LysR family (NCBI ptt file) 393, 469
BC1684 BC1684 ABC transporter ATP-binding protein (NCBI ptt file) 469, 523
BC1685 BC1685 ABC transporter substrate-binding protein (NCBI ptt file) 469, 523
BC1686 BC1686 Zn-dependent hydrolase (beta-lactamase superfamily) (NCBI ptt file) 393, 469
BC1873 BC1873 Phage protein (NCBI ptt file) 46, 469
BC1874 BC1874 Phage protein (NCBI ptt file) 342, 469
BC1876 BC1876 Phage protein (NCBI ptt file) 342, 469
BC1878 BC1878 Phage protein (NCBI ptt file) 202, 469
BC2111 BC2111 hypothetical protein (NCBI ptt file) 241, 393
BC2167 BC2167 Bacillolysin (NCBI ptt file) 321, 393
BC2168 BC2168 hypothetical protein (NCBI ptt file) 46, 393
BC2385 BC2385 Dehydrogenase (NCBI ptt file) 202, 393
BC2452 BC2452 Peptide synthetase (NCBI ptt file) 232, 393
BC3035 BC3035 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 113, 469
BC3036 BC3036 hypothetical protein (NCBI ptt file) 395, 469
BC3099 BC3099 Spore germination protein QA (NCBI ptt file) 186, 393
BC3254 BC3254 Penicillin acylase II (NCBI ptt file) 293, 469
BC3305 BC3305 hypothetical protein (NCBI ptt file) 469, 525
BC3306 BC3306 hypothetical protein (NCBI ptt file) 469, 525
BC3534 BC3534 IG hypothetical 17193 (NCBI ptt file) 393, 487
BC3800 BC3800 Dipicolinate synthase, B chain (NCBI ptt file) 393, 407
BC3991 BC3991 phosphoesterase (NCBI ptt file) 96, 393
BC4043 BC4043 Penicillin-binding protein (NCBI ptt file) 279, 469
BC4978 BC4978 hypothetical protein (NCBI ptt file) 184, 469
BC5293 BC5293 NADH-quinone oxidoreductase chain L (NCBI ptt file) 393, 490
BC5296 BC5296 NADH-quinone oxidoreductase chain I (NCBI ptt file) 321, 393
BC5341 BC5341 Acyl-CoA dehydrogenase, short-chain specific (NCBI ptt file) 229, 469
BC5342 BC5342 Acyl-CoA dehydrogenase, short-chain specific (NCBI ptt file) 229, 469
BC5343 BC5343 3-hydroxybutyryl-CoA dehydrogenase (NCBI ptt file) 229, 469
BC5354 BC5354 ABC transporter permease protein (NCBI ptt file) 398, 469
BC5355 BC5355 ABC transporter ATP-binding protein (NCBI ptt file) 54, 469
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 BC1683
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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