Organism : Bacillus cereus ATCC14579 | Module List :
BC4124

Transcriptional regulator, MarR family (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4124
(Mouseover regulator name to see its description)

BC4124 is regulated by 23 influences and regulates 9 modules.
Regulators for BC4124 (23)
Regulator Module Operator
BC0265 166 tf
BC0518 166 tf
BC0880 166 tf
BC1673 166 tf
BC2358 166 tf
BC4053 166 tf
BC4124 166 tf
BC4170 166 tf
BC4240 166 tf
BC4256 166 tf
BC4703 166 tf
BC5481 166 tf
BC0266 337 tf
BC1680 337 tf
BC3389 337 tf
BC3497 337 tf
BC4124 337 tf
BC4174 337 tf
BC5171 337 tf
BC5173 337 tf
BC5256 337 tf
BC5265 337 tf
BC5409 337 tf

Warning: BC4124 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
4248 1.30e-07 AAGGAGg
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4249 1.30e+04 GAA.GGttCtGctATgC
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4586 2.30e-08 AaaAGGgG
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4587 9.30e+04 GggGGAC
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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 BC4124

BC4124 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC4124

BC4124 has total of 50 gene neighbors in modules 166, 337
Gene neighbors (50)
Gene Common Name Description Module membership
BC0335 BC0335 hypothetical protein (NCBI ptt file) 166, 337
BC0336 BC0336 Somatin-like protein (NCBI ptt file) 103, 337
BC1045 BC1045 hypothetical protein (NCBI ptt file) 166, 296
BC1150 BC1150 IG hypothetical 15940 (NCBI ptt file) 126, 337
BC1188 BC1188 Arsenate reductase family protein (NCBI ptt file) 129, 166
BC1432 BC1432 Proton/sodium-glutamate symport protein (NCBI ptt file) 133, 337
BC1482 BC1482 Riboflavin transporter (NCBI ptt file) 70, 166
BC1510 BC1510 DNA-binding protein HU (NCBI ptt file) 166, 480
BC1562 BC1562 Cell division protein DIVIVA (NCBI ptt file) 166, 380
BC1680 BC1680 Transcriptional regulator, XRE family (NCBI ptt file) 1, 337
BC1689 BC1689 hypothetical protein (NCBI ptt file) 166, 475
BC1755 BC1755 UDP-galactose-lipid carrier transferase (NCBI ptt file) 26, 337
BC2012 BC2012 hypothetical protein (NCBI ptt file) 119, 166
BC2665 BC2665 Teicoplanin resistance protein vanZ (NCBI ptt file) 97, 337
BC2717 BC2717 hypothetical protein (NCBI ptt file) 100, 337
BC2718 BC2718 hypothetical protein (NCBI ptt file) 100, 337
BC2817 BC2817 hypothetical protein (NCBI ptt file) 337, 354
BC2841 BC2841 hypothetical protein (NCBI ptt file) 296, 337
BC2842 BC2842 hypothetical protein (NCBI ptt file) 296, 337
BC3061 BC3061 Penicillin-binding protein (NCBI ptt file) 24, 337
BC3437 BC3437 hypothetical Cytosolic Protein (NCBI ptt file) 313, 337
BC3508 BC3508 hypothetical protein (NCBI ptt file) 128, 337
BC3648 BC3648 CarD-like transcriptional regulator (NCBI ptt file) 98, 337
BC3650 BC3650 Imidazolonepropionase (NCBI ptt file) 138, 337
BC3651 BC3651 Urocanate hydratase (NCBI ptt file) 138, 337
BC3652 BC3652 Histidine ammonia-lyase (NCBI ptt file) 186, 337
BC3661 BC3661 CcdC protein (NCBI ptt file) 166, 187
BC3740 BC3740 ADA regulatory protein (NCBI ptt file) 224, 337
BC3741 BC3741 O6-methylguanine-DNA methyltransferase (NCBI ptt file) 224, 337
BC3742 BC3742 DNA-3-methyladenine glycosylase II (NCBI ptt file) 327, 337
BC3923 BC3923 LSU ribosomal protein L32P (NCBI ptt file) 166, 401
BC3931 BC3931 hypothetical protein (NCBI ptt file) 166, 296
BC4053 BC4053 Transcriptional regulator, GntR family (NCBI ptt file) 166, 401
BC4061 BC4061 Peptidyl-prolyl cis-trans isomerase (NCBI ptt file) 74, 166
BC4124 BC4124 Transcriptional regulator, MarR family (NCBI ptt file) 166, 337
BC4152 BC4152 hypothetical protein (NCBI ptt file) 166, 337
BC4153 BC4153 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 88, 337
BC4245 BC4245 hypothetical protein (NCBI ptt file) 28, 337
BC4256 BC4256 Transcriptional regulator, ArsR family (NCBI ptt file) 74, 166
BC4259 BC4259 hypothetical Membrane Spanning Protein (NCBI ptt file) 1, 166
BC4306 BC4306 GatB/Yqey domain protein (NCBI ptt file) 166, 207
BC4454 BC4454 hypothetical protein (NCBI ptt file) 313, 337
BC4521 BC4521 Thioredoxin (NCBI ptt file) 107, 166
BC4953 BC4953 hypothetical protein (NCBI ptt file) 285, 337
BC4969 BC4969 hypothetical Membrane Spanning Protein (NCBI ptt file) 166, 326
BC5048 BC5048 Ferritin (NCBI ptt file) 1, 337
BC5170 BC5170 Integral membrane protein (NCBI ptt file) 7, 337
BC5171 BC5171 Transcriptional regulator, MerR family (NCBI ptt file) 7, 337
BC5172 BC5172 hypothetical protein (NCBI ptt file) 337, 475
BC5304 BC5304 None 161, 337
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 BC4124
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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