Organism : Bacillus cereus ATCC14579 | Module List :
BC1075

Beta-lactamase repressor (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Predicted transcriptional regulator cog/ cog
DNA binding go/ molecular_function
beta-lactamase activity go/ molecular_function
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 BC1075
(Mouseover regulator name to see its description)

BC1075 is regulated by 25 influences and regulates 5 modules.
Regulators for BC1075 (25)
Regulator Module Operator
BC0758 440 tf
BC0958 440 tf
BC0961 440 tf
BC1033 440 tf
BC1363 440 tf
BC1614 440 tf
BC1724 440 tf
BC2218 440 tf
BC2351 440 tf
BC2558 440 tf
BC2996 440 tf
BC4826 440 tf
BC5352 440 tf
BC0051 219 tf
BC1047 219 tf
BC1075 219 tf
BC1987 219 tf
BC2469 219 tf
BC4010 219 tf
BC4204 219 tf
BC4206 219 tf
BC4603 219 tf
BC5200 219 tf
BC5339 219 tf
BC5368 219 tf

Warning: BC1075 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
4354 9.90e+03 AGGCCG
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4355 1.10e+04 GGATGcACC
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4790 1.40e+01 aggAGGag
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4791 2.40e+04 GCGTGcG
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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 BC1075

BC1075 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted transcriptional regulator cog/ cog
DNA binding go/ molecular_function
beta-lactamase activity go/ molecular_function
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC1075

BC1075 has total of 36 gene neighbors in modules 219, 440
Gene neighbors (36)
Gene Common Name Description Module membership
BC0051 BC0051 Pur operon repressor (NCBI ptt file) 219, 406
BC0193 BC0193 hypothetical protein (NCBI ptt file) 343, 440
BC0645 BC0645 None 364, 440
BC0651 BC0651 Two component system histidine kinase (NCBI ptt file) 440, 478
BC0652 BC0652 Two-component response regulator (NCBI ptt file) 228, 440
BC1014 BC1014 Quinone oxidoreductase (NCBI ptt file) 364, 440
BC1074 BC1074 hypothetical protein (NCBI ptt file) 148, 440
BC1075 BC1075 Beta-lactamase repressor (NCBI ptt file) 219, 440
BC1077 BC1077 Transcriptional regulator, TetR family (NCBI ptt file) 304, 440
BC1130 BC1130 hypothetical protein (NCBI ptt file) 9, 440
BC1336 BC1336 Sporulation kinase D (NCBI ptt file) 6, 440
BC1416 BC1416 CDP-diacylglycerol--serine O-phosphatidyltransferase (NCBI ptt file) 64, 219
BC2558 BC2558 Transcriptional regulator (NCBI ptt file) 7, 440
BC2988 BC2988 Transcriptional regulator, Cro/CI family (NCBI ptt file) 100, 440
BC2996 BC2996 Transcriptional regulator, PadR family (NCBI ptt file) 7, 440
BC3226 BC3226 hypothetical protein (NCBI ptt file) 440, 449
BC3279 BC3279 hypothetical protein (NCBI ptt file) 7, 440
BC3334 BC3334 2-haloalkanoic acid dehalogenase (NCBI ptt file) 15, 440
BC3636 BC3636 hypothetical Cytosolic Protein (NCBI ptt file) 308, 440
BC3924 BC3924 hypothetical Cytosolic Protein (NCBI ptt file) 219, 325
BC3929 BC3929 Phosphopantetheine adenylyltransferase (NCBI ptt file) 170, 219
BC3996 BC3996 hypothetical Exported Protein (NCBI ptt file) 20, 440
BC4282 BC4282 Endonuclease IV (NCBI ptt file) 219, 325
BC4337 BC4337 hypothetical Membrane Spanning Protein (NCBI ptt file) 440, 443
BC4453 BC4453 Phage protein (NCBI ptt file) 62, 440
BC4532 BC4532 hypothetical protein (NCBI ptt file) 7, 440
BC4660 BC4660 Acetoin utilization protein acuA (NCBI ptt file) 440, 478
BC4684 BC4684 UDP-N-acetylmuramate--alanine ligase (NCBI ptt file) 219, 325
BC4740 BC4740 TrkA C-terminal domain protein (NCBI ptt file) 219, 485
BC4933 BC4933 Methyltransferase (NCBI ptt file) 303, 440
BC5011 BC5011 hypothetical protein (NCBI ptt file) 422, 440
BC5352 BC5352 two-component response regulator YocG (NCBI) 41, 440
BC5353 BC5353 Two-component sensor kinase yocF (NCBI ptt file) 41, 440
BC5368 BC5368 Transcriptional regulator pfoR (NCBI ptt file) 219, 403
BC5424 BC5424 Methyl-accepting chemotaxis protein (NCBI ptt file) 416, 440
BC5446 BC5446 None 416, 440
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 BC1075
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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