Organism : Bacillus cereus ATCC14579 | Module List :
BC2367

Transcriptional regulators, LysR family (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2367
(Mouseover regulator name to see its description)

BC2367 is regulated by 28 influences and regulates 5 modules.
Regulators for BC2367 (28)
Regulator Module Operator
BC0158 364 tf
BC0953 364 tf
BC1032 364 tf
BC1253 364 tf
BC2362 364 tf
BC2367 364 tf
BC2470 364 tf
BC2558 364 tf
BC3175 364 tf
BC3244 364 tf
BC3522 364 tf
BC3961 364 tf
BC4212 364 tf
BC4336 364 tf
BC4661 364 tf
BC0099 97 tf
BC0958 97 tf
BC1622 97 tf
BC1932 97 tf
BC2444 97 tf
BC3332 97 tf
BC3400 97 tf
BC3423 97 tf
BC3449 97 tf
BC4029 97 tf
BC4294 97 tf
BC4474 97 tf
BC4611 97 tf

Warning: BC2367 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
4110 8.40e+01 gaAagAGagag
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4111 4.10e+04 CcTGGTcC
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4638 6.60e-04 gaAAgGaGga
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4639 7.10e+02 TTcttctcttTCctctc.ta.tTc
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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 BC2367

BC2367 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC2367

BC2367 has total of 58 gene neighbors in modules 97, 364
Gene neighbors (58)
Gene Common Name Description Module membership
BC0369 BC0369 Zinc metalloprotease (NCBI ptt file) 8, 364
BC0460 BC0460 hypothetical protein (NCBI ptt file) 9, 364
BC0461 BC0461 General stress protein 26 (NCBI ptt file) 160, 364
BC0475 BC0475 None 97, 468
BC0645 BC0645 None 364, 440
BC0780 BC0780 hypothetical protein (NCBI ptt file) 12, 364
BC0781 BC0781 hypothetical protein (NCBI ptt file) 20, 364
BC0835 BC0835 hypothetical protein (NCBI ptt file) 97, 265
BC0885 BC0885 DNA-3-methyladenine glycosylase II (NCBI ptt file) 308, 364
BC0951 BC0951 hypothetical protein (NCBI ptt file) 341, 364
BC0953 BC0953 Transcriptional regulator, MerR family (NCBI ptt file) 364, 454
BC0962 BC0962 Lincomycin resistance protein (NCBI ptt file) 97, 181
BC0980 BC0980 Transcriptional regulator, TetR family (NCBI ptt file) 308, 364
BC1014 BC1014 Quinone oxidoreductase (NCBI ptt file) 364, 440
BC1129 BC1129 Trifolitoxin immunity protein (NCBI ptt file) 97, 364
BC1167 BC1167 hypothetical protein (NCBI ptt file) 97, 452
BC1379 BC1379 Gentamicin resistance protein (NCBI ptt file) 364, 405
BC1388 BC1388 hypothetical protein (NCBI ptt file) 97, 454
BC1622 BC1622 Stage 0 sporulation regulatory protein (NCBI ptt file) 8, 97
BC1623 BC1623 Hfq protein (NCBI ptt file) 85, 97
BC1627 BC1627 Chemotaxis protein cheY (NCBI ptt file) 97, 396
BC1711 BC1711 Short chain dehydrogenase (NCBI ptt file) 364, 475
BC1775 BC1775 None 97, 442
BC1794 BC1794 Oligopeptide-binding protein oppA (NCBI ptt file) 97, 404
BC1800 BC1800 Two-component response regulator vanR (NCBI ptt file) 97, 163
BC1847 BC1847 Transcriptional regulator, MerR family (NCBI ptt file) 97, 401
BC1932 BC1932 Transcriptional regulators, LysR family (NCBI ptt file) 97, 481
BC2097 BC2097 hypothetical protein (NCBI ptt file) 97, 364
BC2269 BC2269 hypothetical protein (NCBI ptt file) 364, 415
BC2318 BC2318 hypothetical protein (NCBI ptt file) 97, 489
BC2367 BC2367 Transcriptional regulators, LysR family (NCBI ptt file) 97, 364
BC2582 BC2582 Terminase small subunit (NCBI ptt file) 138, 364
BC2665 BC2665 Teicoplanin resistance protein vanZ (NCBI ptt file) 97, 337
BC2703 BC2703 hypothetical protein (NCBI ptt file) 97, 148
BC2774 BC2774 hypothetical protein (NCBI ptt file) 97, 160
BC2854 BC2854 Oxidoreductase (NCBI ptt file) 97, 294
BC2876 BC2876 Acetyltransferase (NCBI ptt file) 30, 364
BC2950 BC2950 putative kinase (NCBI ptt file) 7, 364
BC3040 BC3040 EMG2 protein (NCBI ptt file) 97, 225
BC3138 BC3138 hypothetical protein (NCBI ptt file) 85, 364
BC3148 BC3148 Streptothricin acetyltransferase (NCBI ptt file) 63, 364
BC3175 BC3175 Leucine-responsive regulatory protein (NCBI ptt file) 364, 428
BC3232 BC3232 hypothetical protein (NCBI ptt file) 85, 364
BC3238 BC3238 hypothetical protein (NCBI ptt file) 85, 364
BC3309 BC3309 hypothetical Cytosolic Protein (NCBI ptt file) 97, 396
BC3310 BC3310 Transporter, MFS superfamily (NCBI ptt file) 97, 396
BC3423 BC3423 Transcriptional regulator, ArsR family (NCBI ptt file) 97, 220
BC3500 BC3500 hypothetical protein (NCBI ptt file) 97, 155
BC3530 BC3530 Membrane protein, MgtC/SapB family (NCBI ptt file) 35, 364
BC3551 BC3551 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 97, 485
BC3610 BC3610 hypothetical protein (NCBI ptt file) 212, 364
BC3614 BC3614 None 97, 396
BC3961 BC3961 putative transcriptional regulator (NCBI ptt file) 364, 489
BC4404 BC4404 Cobalt-zinc-cadmium resistance protein czcD (NCBI ptt file) 72, 364
BC4611 BC4611 Cytosolic protein containing multiple CBS domains (NCBI ptt file) 97, 489
BC4739 BC4739 Na+/H+ antiporter NapA (NCBI ptt file) 97, 509
BC4741 BC4741 DNA integration/recombination/invertion protein (NCBI ptt file) 97, 265
BC4920 BC4920 hypothetical Membrane Spanning Protein (NCBI ptt file) 26, 364
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 BC2367
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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