Organism : Bacillus cereus ATCC14579 | Module List :
BC0953

Transcriptional regulator, MerR family (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0953
(Mouseover regulator name to see its description)

BC0953 is regulated by 31 influences and regulates 12 modules.
Regulators for BC0953 (31)
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
BC0057 454 tf
BC0114 454 tf
BC0953 454 tf
BC1115 454 tf
BC1329 454 tf
BC2410 454 tf
BC2469 454 tf
BC2517 454 tf
BC2811 454 tf
BC3025 454 tf
BC3408 454 tf
BC3449 454 tf
BC3587 454 tf
BC3961 454 tf
BC4611 454 tf
BC5251 454 tf

Warning: BC0953 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
4638 6.60e-04 gaAAgGaGga
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4639 7.10e+02 TTcttctcttTCctctc.ta.tTc
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4818 5.60e-07 aaggaGggGaataa
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4819 2.60e+01 aCAttcCcctTg
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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 BC0953

BC0953 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC0953

BC0953 has total of 57 gene neighbors in modules 364, 454
Gene neighbors (57)
Gene Common Name Description Module membership
BC0369 BC0369 Zinc metalloprotease (NCBI ptt file) 8, 364
BC0414 BC0414 PTS system, glucose-specific IIBC component (NCBI ptt file) 387, 454
BC0415 BC0415 Exodeoxyribonuclease III (NCBI ptt file) 387, 454
BC0460 BC0460 hypothetical protein (NCBI ptt file) 9, 364
BC0461 BC0461 General stress protein 26 (NCBI ptt file) 160, 364
BC0462 BC0462 Calcium/proton antiporter (NCBI ptt file) 42, 454
BC0645 BC0645 None 364, 440
BC0655 BC0655 Universal stress protein family (NCBI ptt file) 212, 454
BC0780 BC0780 hypothetical protein (NCBI ptt file) 12, 364
BC0781 BC0781 hypothetical protein (NCBI ptt file) 20, 364
BC0842 BC0842 PTS system, sucrose-specific IIBC component (NCBI ptt file) 387, 454
BC0885 BC0885 DNA-3-methyladenine glycosylase II (NCBI ptt file) 308, 364
BC0951 BC0951 hypothetical protein (NCBI ptt file) 341, 364
BC0952 BC0952 hypothetical protein (NCBI ptt file) 316, 454
BC0953 BC0953 Transcriptional regulator, MerR family (NCBI ptt file) 364, 454
BC0963 BC0963 hypothetical protein (NCBI ptt file) 160, 454
BC0980 BC0980 Transcriptional regulator, TetR family (NCBI ptt file) 308, 364
BC0983 BC0983 hypothetical protein (NCBI ptt file) 153, 454
BC1014 BC1014 Quinone oxidoreductase (NCBI ptt file) 364, 440
BC1129 BC1129 Trifolitoxin immunity protein (NCBI ptt file) 97, 364
BC1379 BC1379 Gentamicin resistance protein (NCBI ptt file) 364, 405
BC1388 BC1388 hypothetical protein (NCBI ptt file) 97, 454
BC1442 BC1442 hypothetical protein (NCBI ptt file) 248, 454
BC1600 BC1600 Ribonuclease H (NCBI ptt file) 454, 489
BC1711 BC1711 Short chain dehydrogenase (NCBI ptt file) 364, 475
BC2097 BC2097 hypothetical protein (NCBI ptt file) 97, 364
BC2269 BC2269 hypothetical protein (NCBI ptt file) 364, 415
BC2274 BC2274 hypothetical protein (NCBI ptt file) 160, 454
BC2367 BC2367 Transcriptional regulators, LysR family (NCBI ptt file) 97, 364
BC2518 BC2518 Methyltransferase (NCBI ptt file) 248, 454
BC2582 BC2582 Terminase small subunit (NCBI ptt file) 138, 364
BC2747 BC2747 hypothetical Cytosolic Protein (NCBI ptt file) 238, 454
BC2825 BC2825 hypothetical protein (NCBI ptt file) 248, 454
BC2876 BC2876 Acetyltransferase (NCBI ptt file) 30, 364
BC2950 BC2950 putative kinase (NCBI ptt file) 7, 364
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
BC3328 BC3328 ABC transporter permease protein (NCBI ptt file) 363, 454
BC3330 BC3330 hypothetical protein (NCBI ptt file) 454, 497
BC3350 BC3350 TPR-repeat-containing protein (NCBI ptt file) 160, 454
BC3408 BC3408 Transcriptional regulator, MarR family (NCBI ptt file) 454, 489
BC3433 BC3433 hypothetical protein (NCBI ptt file) 267, 454
BC3449 BC3449 Catabolite gene activator (NCBI ptt file) 454, 489
BC3451 BC3451 hypothetical Membrane Spanning Protein (NCBI ptt file) 454, 496
BC3530 BC3530 Membrane protein, MgtC/SapB family (NCBI ptt file) 35, 364
BC3610 BC3610 hypothetical protein (NCBI ptt file) 212, 364
BC3961 BC3961 putative transcriptional regulator (NCBI ptt file) 364, 489
BC4012 BC4012 Cyclodextrin transport system permease protein (NCBI ptt file) 111, 454
BC4025 BC4025 hypothetical protein (NCBI ptt file) 167, 454
BC4404 BC4404 Cobalt-zinc-cadmium resistance protein czcD (NCBI ptt file) 72, 364
BC4622 BC4622 hypothetical protein (NCBI ptt file) 316, 454
BC4713 BC4713 hypothetical protein (NCBI ptt file) 227, 454
BC4920 BC4920 hypothetical Membrane Spanning Protein (NCBI ptt file) 26, 364
BC5286 BC5286 Transcriptional regulator with ABC transporter ATP-binding domain and LytTR DNA-binding domain (NCBI ptt file) 411, 454
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 BC0953
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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