Organism : Bacillus cereus ATCC14579 | Module List :
BC2218

Transcriptional regulator, RpiR family (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
sugar binding go/ molecular_function
carbohydrate metabolic process go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2218
(Mouseover regulator name to see its description)

BC2218 is regulated by 23 influences and regulates 20 modules.
Regulators for BC2218 (23)
Regulator Module Operator
BC0059 517 tf
BC0649 517 tf
BC0954 517 tf
BC0975 517 tf
BC1531 517 tf
BC1715 517 tf
BC1841 517 tf
BC2218 517 tf
BC3332 517 tf
BC4703 517 tf
BC5175 517 tf
BC0099 214 tf
BC0613 214 tf
BC0954 214 tf
BC1080 214 tf
BC1302 214 tf
BC1363 214 tf
BC2218 214 tf
BC3095 214 tf
BC3706 214 tf
BC3826 214 tf
BC4081 214 tf
BC5000 214 tf

Warning: BC2218 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
4344 7.20e-13 aaaAggGGAga
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4345 6.10e+03 CAGTGGGGG
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4944 9.10e+01 atGtgAAAgggGGgc
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4945 1.10e+03 taaAagggGtG
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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 BC2218

BC2218 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
sugar binding go/ molecular_function
carbohydrate metabolic process go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC2218

BC2218 has total of 56 gene neighbors in modules 214, 517
Gene neighbors (56)
Gene Common Name Description Module membership
BC0059 BC0059 Stage V sporulation protein T (NCBI ptt file) 281, 517
BC0127 BC0127 None 214, 396
BC0559 BC0559 Methyl-accepting chemotaxis protein (NCBI ptt file) 489, 517
BC0692 BC0692 Acetyltransferase (NCBI ptt file) 431, 517
BC0844 BC0844 hypothetical Membrane Spanning Protein (NCBI ptt file) 486, 517
BC0888 BC0888 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 214, 382
BC0959 BC0959 hypothetical Membrane Spanning Protein (NCBI ptt file) 37, 214
BC1072 BC1072 Endonuclease/Exonuclease/phosphatase family protein (NCBI ptt file) 60, 517
BC1139 BC1139 hypothetical Cytosolic Protein (NCBI ptt file) 31, 517
BC1156 BC1156 Ammonium transporter (NCBI ptt file) 214, 481
BC1259 BC1259 hypothetical protein (NCBI ptt file) 62, 214
BC1263 BC1263 Phage integrase family protein (NCBI ptt file) 405, 517
BC1359 BC1359 Bacitracin transport ATP-binding protein bcrA (NCBI ptt file) 341, 517
BC1571 BC1571 hypothetical Membrane Spanning Protein (NCBI ptt file) 204, 214
BC1628 BC1628 Chemotaxis protein cheA (NCBI ptt file) 214, 517
BC1639 BC1639 Flagellar protein fliS (NCBI ptt file) 214, 396
BC1715 BC1715 Transcriptional regulator (NCBI ptt file) 369, 517
BC1716 BC1716 Na+ driven multidrug efflux pump (NCBI ptt file) 369, 517
BC1752 BC1752 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 214, 428
BC1761 BC1761 GTP-binding protein hflX (NCBI ptt file) 75, 517
BC1996 BC1996 Transcription state regulatory protein abrB (NCBI ptt file) 100, 517
BC2095 BC2095 hypothetical protein (NCBI ptt file) 341, 517
BC2160 BC2160 hypothetical protein (NCBI ptt file) 139, 517
BC2212 BC2212 hypothetical protein (NCBI ptt file) 76, 517
BC2218 BC2218 Transcriptional regulator, RpiR family (NCBI ptt file) 214, 517
BC2221 BC2221 Oligopeptide transport system permease protein oppC (NCBI ptt file) 288, 517
BC2261 BC2261 Cobalt-zinc-cadmium resistance protein czcD (NCBI ptt file) 100, 214
BC2333 BC2333 hypothetical protein (NCBI ptt file) 214, 266
BC2375 BC2375 hypothetical protein (NCBI ptt file) 509, 517
BC2392 BC2392 FenI (NCBI ptt file) 241, 517
BC2464 BC2464 S-layer protein / Peptidoglycan endo-beta-N-acetylglucosaminidase (NCBI ptt file) 139, 517
BC2666 BC2666 hypothetical protein (NCBI ptt file) 396, 517
BC2726 BC2726 hypothetical protein (NCBI ptt file) 509, 517
BC2727 BC2727 hypothetical protein (NCBI ptt file) 431, 517
BC3055 BC3055 hypothetical protein (NCBI ptt file) 363, 517
BC3088 BC3088 Metal-dependent hydrolase (NCBI ptt file) 60, 517
BC3121 BC3121 5'-nucleotidase (NCBI ptt file) 214, 428
BC3250 BC3250 hypothetical protein (NCBI ptt file) 214, 341
BC3331 BC3331 hypothetical protein (NCBI ptt file) 7, 517
BC3398 BC3398 Serine transporter (NCBI ptt file) 214, 481
BC3536 BC3536 hypothetical protein (NCBI ptt file) 7, 517
BC3618 BC3618 Peptidoglycan N-acetylglucosamine deacetylase (NCBI ptt file) 30, 517
BC3639 BC3639 hypothetical Membrane Spanning Protein (NCBI ptt file) 214, 428
BC4232 BC4232 Shikimate kinase (NCBI ptt file) 246, 517
BC4385 BC4385 hypothetical Membrane Spanning Protein (NCBI ptt file) 134, 517
BC4466 BC4466 CotS-related protein (NCBI ptt file) 256, 517
BC4687 BC4687 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 214, 341
BC4708 BC4708 Transcriptional regulator, ArsR family (NCBI ptt file) 198, 214
BC4709 BC4709 hypothetical protein (NCBI ptt file) 198, 214
BC4944 BC4944 hypothetical protein (NCBI ptt file) 214, 481
BC5000 BC5000 Transcriptional regulator, TetR family (NCBI ptt file) 214, 341
BC5001 BC5001 Metal-dependent hydrolase (NCBI ptt file) 214, 341
BC5034 BC5034 Methyl-accepting chemotaxis protein (NCBI ptt file) 214, 266
BC5158 BC5158 Integral membrane protein (NCBI ptt file) 92, 214
BC5263 BC5263 UDP-glucose 4-epimerase (NCBI ptt file) 204, 214
BC5490 BC5490 LSU ribosomal protein L34P (NCBI ptt file) 7, 517
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 BC2218
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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