Organism : Bacillus cereus ATCC14579 | Module List :
BC4652

Transcriptional regulator IcaR (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4652
(Mouseover regulator name to see its description)

BC4652 is regulated by 26 influences and regulates 37 modules.
Regulators for BC4652 (26)
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
BC0498 422 tf
BC0680 422 tf
BC1080 422 tf
BC1695 422 tf
BC1841 422 tf
BC2672 422 tf
BC2738 422 tf
BC3062 422 tf
BC3356 422 tf
BC3813 422 tf
BC4072 422 tf
BC4652 422 tf
BC4703 422 tf
BC5038 422 tf
BC5481 422 tf
Regulated by BC4652 (37)
Module Residual Genes
3 0.43 22
19 0.33 19
48 0.51 21
60 0.42 31
67 0.43 22
73 0.43 25
75 0.40 19
92 0.37 18
120 0.42 25
129 0.37 23
139 0.49 32
143 0.36 21
173 0.31 22
180 0.31 19
187 0.44 25
194 0.47 23
203 0.40 23
211 0.32 19
213 0.44 31
222 0.46 20
224 0.47 22
225 0.62 34
245 0.56 24
284 0.57 35
302 0.48 20
322 0.36 23
333 0.39 24
347 0.44 20
381 0.41 29
421 0.53 8
422 0.38 22
425 0.39 21
434 0.55 27
438 0.43 25
488 0.41 24
491 0.49 34
497 0.38 21
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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4754 2.30e-01 AgAaAagGgta
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4755 5.60e+01 caaGaGGAa.accaAgTggttTcg
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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 BC4652

BC4652 is enriched for 5 functions in 3 categories.
Module neighborhood information for BC4652

BC4652 has total of 42 gene neighbors in modules 173, 422
Gene neighbors (42)
Gene Common Name Description Module membership
BC0053 BC0053 Stage V sporulation protein G (NCBI ptt file) 216, 422
BC0237 BC0237 Galactose-1-phosphate uridylyltransferase (NCBI ptt file) 98, 173
BC0387 BC0387 hypothetical protein (NCBI ptt file) 173, 211
BC0498 BC0498 Regulatory protein recX (NCBI ptt file) 422, 475
BC0540 BC0540 Mutator mutT protein (7,8-dihydro-8-oxoguanine-triphosphatase) (NCBI ptt file) 422, 491
BC0972 BC0972 hypothetical protein (NCBI ptt file) 211, 422
BC0982 BC0982 hypothetical protein (NCBI ptt file) 333, 422
BC1066 BC1066 Signal transduction protein TRAP (NCBI ptt file) 173, 233
BC1464 BC1464 hypothetical protein (NCBI ptt file) 173, 211
BC1467 BC1467 hypothetical protein (NCBI ptt file) 173, 211
BC1605 BC1605 Transporter, LysE family (NCBI ptt file) 333, 422
BC1606 BC1606 hypothetical Cytosolic Protein (NCBI ptt file) 211, 422
BC1692 BC1692 hypothetical protein (NCBI ptt file) 173, 422
BC1717 BC1717 Peptidase E (NCBI ptt file) 173, 211
BC1771 BC1771 Fibronectin-binding protein (NCBI ptt file) 294, 422
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
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
BC2579 BC2579 hypothetical Cytosolic Protein (NCBI ptt file) 173, 211
BC2738 BC2738 Transcriptional regulator, AraC family (NCBI ptt file) 173, 203
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
BC3672 BC3672 hypothetical protein (NCBI ptt file) 173, 409
BC3880 BC3880 hypothetical Membrane Spanning Protein (NCBI ptt file) 333, 422
BC3881 BC3881 Phosphoglycolate phosphatase (NCBI ptt file) 333, 422
BC4030 BC4030 D-beta-hydroxybutyrate dehydrogenase (NCBI ptt file) 173, 211
BC4144 BC4144 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 173, 211
BC4167 BC4167 Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) 129, 422
BC4652 BC4652 Transcriptional regulator IcaR (NCBI ptt file) 173, 422
BC4754 BC4754 putative acetyltransferase/acyltransferase (NCBI ptt file) 129, 422
BC4776 BC4776 hypothetical protein (NCBI ptt file) 216, 422
BC4971 BC4971 Phosphoglycerate mutase (NCBI ptt file) 73, 422
BC4972 BC4972 DNA-binding protein (NCBI ptt file) 73, 422
BC4993 BC4993 hypothetical lipoprotein (NCBI ptt file) 333, 422
BC5011 BC5011 hypothetical protein (NCBI ptt file) 422, 440
BC5322 BC5322 Nitrilotriacetate monooxygenase component B (NCBI ptt file) 173, 409
BC5417 BC5417 Two-component response regulator (NCBI ptt file) 422, 473
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 BC4652
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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