Organism : Bacillus cereus ATCC14579 | Module List :
BC4256

Transcriptional regulator, ArsR family (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Predicted 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 BC4256
(Mouseover regulator name to see its description)

BC4256 is regulated by 26 influences and regulates 39 modules.
Regulators for BC4256 (26)
Regulator Module Operator
BC0042 74 tf
BC0648 74 tf
BC0880 74 tf
BC1356 74 tf
BC1603 74 tf
BC2358 74 tf
BC4001 74 tf
BC4124 74 tf
BC4256 74 tf
BC4670 74 tf
BC4703 74 tf
BC5010 74 tf
BC5024 74 tf
BC5481 74 tf
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

Warning: BC4256 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
4068 8.60e+00 TCACCTc
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4069 6.50e+03 GGGGCG
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4248 1.30e-07 AAGGAGg
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4249 1.30e+04 GAA.GGttCtGctATgC
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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 BC4256

BC4256 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted 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 BC4256

BC4256 has total of 41 gene neighbors in modules 74, 166
Gene neighbors (41)
Gene Common Name Description Module membership
BC0042 BC0042 Transcription state regulatory protein abrB (NCBI ptt file) 28, 74
BC0335 BC0335 hypothetical protein (NCBI ptt file) 166, 337
BC0792 BC0792 hypothetical Cytosolic Protein (NCBI ptt file) 74, 119
BC1045 BC1045 hypothetical protein (NCBI ptt file) 166, 296
BC1177 BC1177 None 7, 74
BC1188 BC1188 Arsenate reductase family protein (NCBI ptt file) 129, 166
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
BC1689 BC1689 hypothetical protein (NCBI ptt file) 166, 475
BC2012 BC2012 hypothetical protein (NCBI ptt file) 119, 166
BC2019 BC2019 Low-affinity zinc transport protein (NCBI ptt file) 74, 180
BC3389 BC3389 Transcriptional regulator, MarR family (NCBI ptt file) 1, 74
BC3661 BC3661 CcdC protein (NCBI ptt file) 166, 187
BC3728 BC3728 DNA-binding protein HU (NCBI ptt file) 74, 227
BC3732 BC3732 hypothetical Cytosolic Protein (NCBI ptt file) 74, 415
BC3923 BC3923 LSU ribosomal protein L32P (NCBI ptt file) 166, 401
BC3931 BC3931 hypothetical protein (NCBI ptt file) 166, 296
BC3995 BC3995 hypothetical Cytosolic Protein (NCBI ptt file) 74, 438
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
BC4145 BC4145 hypothetical protein (NCBI ptt file) 74, 119
BC4152 BC4152 hypothetical protein (NCBI ptt file) 166, 337
BC4256 BC4256 Transcriptional regulator, ArsR family (NCBI ptt file) 74, 166
BC4259 BC4259 hypothetical Membrane Spanning Protein (NCBI ptt file) 1, 166
BC4263 BC4263 LSU ribosomal protein L33P (NCBI ptt file) 74, 501
BC4306 BC4306 GatB/Yqey domain protein (NCBI ptt file) 166, 207
BC4521 BC4521 Thioredoxin (NCBI ptt file) 107, 166
BC4702 BC4702 Xaa-His dipeptidase (NCBI ptt file) 74, 119
BC4722 BC4722 Molybdenum cofactor biosynthesis protein C (NCBI ptt file) 74, 399
BC4757 BC4757 Molybdopterin-guanine dinucleotide biosynthesis protein A (NCBI ptt file) 74, 119
BC4909 BC4909 Kinase-associated protein B (NCBI ptt file) 74, 227
BC4969 BC4969 hypothetical Membrane Spanning Protein (NCBI ptt file) 166, 326
BC4991 BC4991 Glycine cleavage system H protein (NCBI ptt file) 74, 126
BC5047 BC5047 IG hypothetical 16995 (NCBI ptt file) 1, 74
BC5165 BC5165 Integral membrane protein (NCBI ptt file) 74, 273
BC5280 BC5280 (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase (NCBI ptt file) 74, 264
BC5320 BC5320 PTS system, glucose-specific IIA component (NCBI ptt file) 74, 199
BC5387 BC5387 Phosphate acetyltransferase (NCBI ptt file) 74, 198
BC5388 BC5388 IG hypothetical 16794 (NCBI ptt file) 74, 227
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 BC4256
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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