Organism : Bacillus cereus ATCC14579 | Module List :
BC2738

Transcriptional regulator, AraC family (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
DNA gyrase inhibitor cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2738
(Mouseover regulator name to see its description)

BC2738 is regulated by 25 influences and regulates 23 modules.
Regulators for BC2738 (25)
Regulator Module Operator
BC0123 173 tf
BC1080 173 tf
BC1710 173 tf
BC1915 173 tf
BC2672 173 tf
BC2738 173 tf
BC3814 173 tf
BC4072 173 tf
BC4652 173 tf
BC5197 173 tf
BC5481 173 tf
BC0123 203 tf
BC0473 203 tf
BC0953 203 tf
BC1037 203 tf
BC1915 203 tf
BC2386 203 tf
BC2672 203 tf
BC2738 203 tf
BC2794 203 tf
BC3244 203 tf
BC4072 203 tf
BC4073 203 tf
BC4652 203 tf
BC4902 203 tf

Warning: BC2738 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
4262 1.80e-03 AGGgGa
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4263 9.70e+03 CCTCCCG
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4322 1.60e-07 aGgatTttaa.tat.TatataGAA
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4323 1.80e-01 AggGGAGga
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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 BC2738

BC2738 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
DNA gyrase inhibitor cog/ cog
Module neighborhood information for BC2738

BC2738 has total of 41 gene neighbors in modules 173, 203
Gene neighbors (41)
Gene Common Name Description Module membership
BC0237 BC0237 Galactose-1-phosphate uridylyltransferase (NCBI ptt file) 98, 173
BC0387 BC0387 hypothetical protein (NCBI ptt file) 173, 211
BC1066 BC1066 Signal transduction protein TRAP (NCBI ptt file) 173, 233
BC1079 BC1079 hypothetical protein (NCBI ptt file) 203, 211
BC1338 BC1338 Oligoendopeptidase F (NCBI ptt file) 203, 395
BC1464 BC1464 hypothetical protein (NCBI ptt file) 173, 211
BC1467 BC1467 hypothetical protein (NCBI ptt file) 173, 211
BC1566 BC1566 Thermostable carboxypeptidase 1 (NCBI ptt file) 203, 299
BC1594 BC1594 Isochorismatase (NCBI ptt file) 203, 395
BC1692 BC1692 hypothetical protein (NCBI ptt file) 173, 422
BC1717 BC1717 Peptidase E (NCBI ptt file) 173, 211
BC1915 BC1915 Transcriptional regulator, PBSX family (NCBI ptt file) 203, 422
BC1947 BC1947 hypothetical protein (NCBI ptt file) 173, 420
BC2112 BC2112 None 173, 233
BC2182 BC2182 Histidinol-phosphatase (NCBI ptt file) 203, 395
BC2183 BC2183 Acetyltransferase (NCBI ptt file) 203, 395
BC2235 BC2235 hypothetical protein (NCBI ptt file) 203, 422
BC2292 BC2292 3-hydroxyisobutyryl-coenzyme A hydrolase (NCBI ptt file) 173, 203
BC2524 BC2524 Oligoendopeptidase F (NCBI ptt file) 173, 203
BC2533 BC2533 Methyltransferase (NCBI ptt file) 173, 211
BC2534 BC2534 hypothetical Membrane Associated Protein (NCBI ptt file) 203, 211
BC2579 BC2579 hypothetical Cytosolic Protein (NCBI ptt file) 173, 211
BC2658 BC2658 Serine/threonine protein kinase (NCBI ptt file) 203, 409
BC2697 BC2697 Translation initiation inhibitor (NCBI ptt file) 203, 299
BC2737 BC2737 hypothetical protein (NCBI ptt file) 203, 299
BC2738 BC2738 Transcriptional regulator, AraC family (NCBI ptt file) 173, 203
BC2782 BC2782 Glutamate-rich protein grpB (NCBI ptt file) 203, 299
BC3057 BC3057 Methyltransferase (NCBI ptt file) 173, 203
BC3453 BC3453 N-acyl homoserine lactone hydrolase (NCBI ptt file) 173, 180
BC3473 BC3473 Aminoglycoside N6'-acetyltransferase (NCBI ptt file) 173, 211
BC3549 BC3549 Acetyltransferase (NCBI ptt file) 203, 211
BC3672 BC3672 hypothetical protein (NCBI ptt file) 173, 409
BC4030 BC4030 D-beta-hydroxybutyrate dehydrogenase (NCBI ptt file) 173, 211
BC4072 BC4072 RNA polymerase sigma-F factor (NCBI ptt file) 203, 420
BC4073 BC4073 Anti-sigma F factor (NCBI ptt file) 203, 491
BC4074 BC4074 Anti-sigma F factor antagonist (NCBI ptt file) 203, 409
BC4144 BC4144 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 173, 211
BC4613 BC4613 Metal-dependent hydrolase (NCBI ptt file) 203, 216
BC4652 BC4652 Transcriptional regulator IcaR (NCBI ptt file) 173, 422
BC5019 BC5019 Ribosomal-protein-serine acetyltransferase (NCBI ptt file) 203, 211
BC5322 BC5322 Nitrilotriacetate monooxygenase component B (NCBI ptt file) 173, 409
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 BC2738
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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