Organism : Bacillus cereus ATCC14579 | Module List :
BC4277

Zinc-specific metalloregulatory protein (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Fe2+/Zn2+ uptake regulation proteins 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 BC4277
(Mouseover regulator name to see its description)

BC4277 is regulated by 24 influences and regulates 8 modules.
Regulators for BC4277 (24)
Regulator Module Operator
BC0116 169 tf
BC0586 169 tf
BC1387 169 tf
BC3400 169 tf
BC3814 169 tf
BC3976 169 tf
BC4170 169 tf
BC4277 169 tf
BC4289 169 tf
BC4670 169 tf
BC4859 169 tf
BC5010 169 tf
BC0265 505 tf
BC0586 505 tf
BC1302 505 tf
BC1329 505 tf
BC3025 505 tf
BC4211 505 tf
BC4277 505 tf
BC4294 505 tf
BC4314 505 tf
BC4589 505 tf
BC4603 505 tf
BC5463 505 tf

Warning: BC4277 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
4254 1.40e+00 TttTaTtA.gAggaaAAtaAg
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4255 5.60e+03 AGgAGGaT
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4920 9.30e-02 GtaGAgGTGAacg
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4921 2.10e+02 AaagGAg.aG
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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 BC4277

BC4277 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Fe2+/Zn2+ uptake regulation proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC4277

BC4277 has total of 30 gene neighbors in modules 169, 505
Gene neighbors (30)
Gene Common Name Description Module membership
BC0257 BC0257 D-alanine--D-alanine ligase (NCBI ptt file) 169, 325
BC0445 BC0445 TerC-like protein (NCBI ptt file) 169, 326
BC0539 BC0539 hypothetical protein (RefSeq) 41, 169
BC0587 BC0587 Acetyltransferase (NCBI ptt file) 118, 169
BC0684 BC0684 Di-/tripeptide transporter (NCBI ptt file) 169, 426
BC0778 BC0778 Thioredoxin (NCBI ptt file) 169, 274
BC0817 BC0817 hypothetical Membrane Spanning Protein (NCBI ptt file) 306, 505
BC1483 BC1483 Ferredoxin (NCBI ptt file) 169, 326
BC1581 BC1581 Mg(2+) P-type ATPase-like protein (NCBI ptt file) 70, 505
BC3311 BC3311 hypothetical protein (NCBI ptt file) 414, 505
BC3642 BC3642 Carboxylesterase (NCBI ptt file) 33, 505
BC3649 BC3649 None 414, 505
BC4277 BC4277 Zinc-specific metalloregulatory protein (NCBI ptt file) 169, 505
BC4278 BC4278 High-affinity zinc uptake system membrane protein znuB (NCBI ptt file) 169, 371
BC4279 BC4279 High-affinity zinc uptake system ATP-binding protein znuC (NCBI ptt file) 169, 505
BC4280 BC4280 hypothetical Membrane Spanning Protein (NCBI ptt file) 169, 326
BC4390 BC4390 Tetratricopeptide repeat family protein (NCBI ptt file) 118, 505
BC4599 BC4599 Pyruvate kinase (NCBI ptt file) 169, 471
BC4600 BC4600 6-phosphofructokinase (NCBI ptt file) 169, 513
BC4653 BC4653 GAF domain-containing proteins (NCBI ptt file) 399, 505
BC4692 BC4692 hypothetical protein (NCBI ptt file) 302, 505
BC4775 BC4775 Phosphoglycerol transferase (NCBI ptt file) 439, 505
BC4919 BC4919 Phosphoglucomutase (NCBI ptt file) 169, 326
BC5043 BC5043 Sodium/proton-dependent alanine carrier protein (NCBI ptt file) 169, 326
BC5107 BC5107 Two-component response regulator (NCBI ptt file) 268, 505
BC5128 BC5128 SsrA-binding protein (NCBI ptt file) 1, 505
BC5130 BC5130 Carboxylesterase (NCBI ptt file) 261, 505
BC5157 BC5157 Mutator mutT protein (7,8-dihydro-8-oxoguanine-triphosphatase) (NCBI ptt file) 374, 505
BC5335 BC5335 Fructose-bisphosphate aldolase (NCBI ptt file) 169, 326
BC5373 BC5373 Transcriptional regulator, MerR family (NCBI ptt file) 261, 505
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 BC4277
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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