Organism : Bacillus cereus ATCC14579 | Module List :
BC1969

Transcriptional regulator, LytR family (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Transcriptional regulator cog/ cog
lytR_cpsA_psr tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1969
(Mouseover regulator name to see its description)

BC1969 is regulated by 17 influences and regulates 9 modules.
Regulators for BC1969 (17)
Regulator Module Operator
BC0975 124 tf
BC1719 124 tf
BC1818 124 tf
BC1969 124 tf
BC2109 124 tf
BC4930 124 tf
BC5173 124 tf
BC5363 124 tf
BC0659 18 tf
BC1053 18 tf
BC1439 18 tf
BC1449 18 tf
BC1969 18 tf
BC2936 18 tf
BC3244 18 tf
BC3589 18 tf
BC4212 18 tf
Regulated by BC1969 (9)
Module Residual Genes
18 0.47 25
72 0.56 36
98 0.50 28
124 0.32 20
305 0.33 23
345 0.29 17
389 0.55 11
415 0.55 30
500 0.33 22
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3958 1.90e-18 AcAAaaatGTAAggtaaaTGtAAg
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3959 2.40e+00 GAAGGGGacaG
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4164 2.60e-40 CTTACAAAAaTGTAAgGTt.aTGT
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4165 1.50e-02 aAaa.a.AtaagAGGtgAag.aa
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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 BC1969

BC1969 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Transcriptional regulator cog/ cog
lytR_cpsA_psr tigr/ tigrfam
Module neighborhood information for BC1969

BC1969 has total of 42 gene neighbors in modules 18, 124
Gene neighbors (42)
Gene Common Name Description Module membership
BC0233 BC0233 hypothetical protein (NCBI ptt file) 124, 500
BC0236 BC0236 Transglycosylase (NCBI ptt file) 18, 475
BC0541 BC0541 Monofunctional biosynthetic peptidoglycan transglycosylase (NCBI ptt file) 18, 455
BC0814 BC0814 ABC transporter permease protein (NCBI ptt file) 124, 500
BC0815 BC0815 ABC transporter ATP-binding protein (NCBI ptt file) 124, 500
BC0816 BC0816 periplasmic component of efflux system (NCBI ptt file) 124, 500
BC1036 BC1036 Glycerol-3-phosphate dehydrogenase (NCBI ptt file) 18, 329
BC1053 BC1053 Transcriptional regulator, TetR family (NCBI ptt file) 18, 369
BC1054 BC1054 hypothetical protein (NCBI ptt file) 18, 369
BC1437 BC1437 Transporter yvqF (NCBI ptt file) 18, 222
BC1438 BC1438 Two-component sensor protein yvqE (NCBI ptt file) 18, 222
BC1618 BC1618 hypothetical Membrane Spanning Protein (NCBI ptt file) 124, 500
BC1969 BC1969 Transcriptional regulator, LytR family (NCBI ptt file) 18, 124
BC1995 BC1995 ABC transporter permease protein (NCBI ptt file) 124, 500
BC2323 BC2323 ABC transporter ATP-binding protein (NCBI ptt file) 18, 124
BC2324 BC2324 ABC transporter permease protein (NCBI ptt file) 18, 124
BC2438 BC2438 hypothetical Cytosolic Protein (NCBI ptt file) 124, 500
BC2689 BC2689 Oxalate/formate antiporter (NCBI ptt file) 18, 88
BC2936 BC2936 Transcriptional repressor Bm3R1 (NCBI ptt file) 18, 369
BC3181 BC3181 hypothetical protein (NCBI ptt file) 124, 500
BC3182 BC3182 hypothetical protein (NCBI ptt file) 124, 500
BC3396 BC3396 hypothetical Membrane Spanning Protein (NCBI ptt file) 18, 122
BC4055 BC4055 N-acetylgalactosamine-6-phosphate deacetylase (NCBI ptt file) 18, 385
BC4212 BC4212 Transcriptional regulator, TetR family (NCBI ptt file) 18, 369
BC4213 BC4213 Quaternary ammonium compound-resistance protein (NCBI ptt file) 18, 369
BC4214 BC4214 Quaternary ammonium compound-resistance protein (NCBI ptt file) 18, 369
BC4215 BC4215 hypothetical protein (NCBI ptt file) 18, 369
BC4482 BC4482 hypothetical protein (NCBI ptt file) 124, 500
BC4742 BC4742 ABC transporter permease protein (NCBI ptt file) 124, 500
BC4743 BC4743 ABC transporter ATP-binding protein (NCBI ptt file) 18, 500
BC4744 BC4744 hypothetical Membrane Spanning Protein (NCBI ptt file) 18, 500
BC4802 BC4802 hypothetical protein (NCBI ptt file) 124, 500
BC4813 BC4813 hypothetical protein (NCBI ptt file) 124, 500
BC4830 BC4830 ABC transporter permease protein (NCBI ptt file) 124, 500
BC4831 BC4831 ABC transporter ATP-binding protein (NCBI ptt file) 124, 500
BC4932 BC4932 hypothetical Membrane Associated Protein (NCBI ptt file) 124, 500
BC4994 BC4994 Ser/Thr and Tyr protein phosphatase (dual specificity) (NCBI ptt file) 18, 122
BC5025 BC5025 Alkaline phosphatase like protein (NCBI ptt file) 18, 500
BC5100 BC5100 hypothetical protein (NCBI ptt file) 124, 500
BC5229 BC5229 hypothetical Membrane Spanning Protein (NCBI ptt file) 18, 500
BC5367 BC5367 hypothetical protein (NCBI ptt file) 18, 500
BC5383 BC5383 Ferrichrome transport system permease protein fhuB (NCBI ptt file) 18, 467
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 BC1969
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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