Organism : Bacillus cereus ATCC14579 | Module List :
BC1083

Transcriptional regulator, LacI family (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
alanine racemase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1083
(Mouseover regulator name to see its description)

BC1083 is regulated by 25 influences and regulates 4 modules.
Regulators for BC1083 (25)
Regulator Module Operator
BC0410 387 tf
BC0613 387 tf
BC0659 387 tf
BC1083 387 tf
BC1335 387 tf
BC2469 387 tf
BC2794 387 tf
BC4433 387 tf
BC4474 387 tf
BC4570 387 tf
BC4611 387 tf
BC4960 387 tf
BC1083 516 tf
BC1335 516 tf
BC2178 516 tf
BC2469 516 tf
BC2794 516 tf
BC2837 516 tf
BC3039 516 tf
BC3160 516 tf
BC3588 516 tf
BC4474 516 tf
BC4661 516 tf
BC5251 516 tf
BC5340 516 tf

Warning: BC1083 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
4684 3.00e-23 tAtGAAAaCGcTtaCa
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4685 5.90e-06 aggGtGGA
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4942 2.70e-06 AtgaAAaCGctTaC
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4943 9.00e-04 aGgGGGgA
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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 BC1083

BC1083 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
alanine racemase activity go/ molecular_function
Module neighborhood information for BC1083

BC1083 has total of 40 gene neighbors in modules 387, 516
Gene neighbors (40)
Gene Common Name Description Module membership
BC0338 BC0338 hypothetical protein (NCBI ptt file) 387, 391
BC0378 BC0378 5-methylthioribose kinase (NCBI ptt file) 387, 516
BC0379 BC0379 Methylthioribose salvage protein (NCBI ptt file) 307, 516
BC0380 BC0380 L-fuculose phosphate aldolase (NCBI ptt file) 387, 516
BC0414 BC0414 PTS system, glucose-specific IIBC component (NCBI ptt file) 387, 454
BC0415 BC0415 Exodeoxyribonuclease III (NCBI ptt file) 387, 454
BC0560 BC0560 Two component system histidine kinase (NCBI ptt file) 489, 516
BC0592 BC0592 Alanine dehydrogenase (NCBI ptt file) 234, 387
BC0631 BC0631 PTS system, trehalose-specific IIBC component (NCBI ptt file) 283, 387
BC0632 BC0632 Trehalose-6-phosphate hydrolase (NCBI ptt file) 283, 387
BC0774 BC0774 Sucrose-6-phosphate hydrolase (NCBI ptt file) 387, 478
BC0775 BC0775 PTS system, sucrose-specific IIBC component (NCBI ptt file) 387, 478
BC0807 BC0807 PTS system, diacetylchitobiose-specific IIA component (NCBI ptt file) 234, 387
BC0808 BC0808 PTS system, diacetylchitobiose-specific IIB component (NCBI ptt file) 387, 516
BC0809 BC0809 PTS system, diacetylchitobiose-specific IIC component (NCBI ptt file) 199, 387
BC0841 BC0841 Glucokinase regulatory protein (NCBI ptt file) 80, 387
BC0842 BC0842 PTS system, sucrose-specific IIBC component (NCBI ptt file) 387, 454
BC0843 BC0843 outer surface protein (NCBI ptt file) 80, 387
BC1034 BC1034 Glycerol uptake facilitator protein (NCBI ptt file) 199, 516
BC1083 BC1083 Transcriptional regulator, LacI family (NCBI ptt file) 387, 516
BC1185 BC1185 Oligopeptide-binding protein oppA (NCBI ptt file) 199, 387
BC1328 BC1328 Saccharopine dehydrogenase [NADP+, L-lysine forming] (NCBI ptt file) 469, 516
BC1440 BC1440 hypothetical protein (NCBI ptt file) 80, 387
BC2238 BC2238 hypothetical protein (NCBI ptt file) 387, 516
BC2851 BC2851 hypothetical protein (NCBI ptt file) 199, 516
BC3197 BC3197 Tetracycline resistance determinant tetV (NCBI ptt file) 324, 516
BC3531 BC3531 Acetyltransferase (NCBI ptt file) 23, 516
BC3718 BC3718 PTS system, fructose-specific IIABC component (NCBI ptt file) 387, 516
BC4526 BC4526 acyl-CoA synthase (RefSeq) 358, 387
BC4661 BC4661 Acetoin utilization acuB protein (NCBI ptt file) 30, 516
BC4662 BC4662 Acetoin utilization acuC protein (NCBI ptt file) 424, 516
BC4814 BC4814 hypothetical protein (NCBI ptt file) 234, 387
BC4841 BC4841 2-keto-3-deoxygluconate permease (NCBI ptt file) 384, 516
BC4843 BC4843 2-dehydro-3-deoxygluconokinase (NCBI ptt file) 387, 516
BC4844 BC4844 4-Hydroxy-2-oxoglutarate aldolase (NCBI ptt file) 387, 516
BC4845 BC4845 L-seryl-tRNA(Sec) selenium transferase (NCBI ptt file) 387, 516
BC4846 BC4846 Dihydroorotase (NCBI ptt file) 387, 516
BC5209 BC5209 6-phospho-beta-glucosidase (NCBI ptt file) 54, 516
BC5211 BC5211 PTS system, lichenan oligosaccharide-specific IIC component (NCBI ptt file) 387, 516
BC5228 BC5228 L-lactate permease (NCBI ptt file) 387, 516
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 BC1083
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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