Organism : Bacillus cereus ATCC14579 | Module List :
BC4952

NifU protein (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Thioredoxin-like proteins and domains cog/ cog
iron ion binding go/ molecular_function
iron-sulfur cluster assembly go/ biological_process
iron-sulfur cluster binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4952
(Mouseover regulator name to see its description)

BC4952 is regulated by 28 influences and regulates 0 modules.
Regulators for BC4952 (28)
Regulator Module Operator
BC0122 216 tf
BC0776 216 tf
BC0880 216 tf
BC1732 216 tf
BC3244 216 tf
BC3653 216 tf
BC3758 216 tf
BC3814 216 tf
BC4104 216 tf
BC4703 216 tf
BC4826 216 tf
BC5010 216 tf
BC5481 216 tf
BC0265 1 tf
BC0880 1 tf
BC1680 1 tf
BC1710 1 tf
BC3389 1 tf
BC4001 1 tf
BC4076 1 tf
BC4211 1 tf
BC4670 1 tf
BC4703 1 tf
BC4826 1 tf
BC4902 1 tf
BC5143 1 tf
BC5197 1 tf
BC5481 1 tf

Warning: BC4952 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
3924 2.00e-05 g.aaaa.aggGGaGa
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3925 1.40e+04 GGCaAaGAGCcaCTC
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4348 1.30e-02 ataaaagGgGG
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4349 2.40e+04 CcaGGCGAAcC
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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 BC4952

BC4952 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Thioredoxin-like proteins and domains cog/ cog
iron ion binding go/ molecular_function
iron-sulfur cluster assembly go/ biological_process
iron-sulfur cluster binding go/ molecular_function
Module neighborhood information for BC4952

BC4952 has total of 51 gene neighbors in modules 1, 216
Gene neighbors (51)
Gene Common Name Description Module membership
BC0053 BC0053 Stage V sporulation protein G (NCBI ptt file) 216, 422
BC0185 BC0185 Arginase (NCBI ptt file) 216, 264
BC0223 BC0223 hypothetical protein (NCBI ptt file) 216, 246
BC0290 BC0290 ABC transporter ATP-binding protein uup (NCBI ptt file) 1, 475
BC0397 BC0397 hypothetical Cytosolic Protein (NCBI ptt file) 129, 216
BC0520 BC0520 hypothetical protein (NCBI ptt file) 216, 264
BC0626 BC0626 Cardiolipin synthetase (NCBI ptt file) 1, 224
BC1052 BC1052 Protein ecsC (NCBI ptt file) 216, 284
BC1255 BC1255 hypothetical protein (NCBI ptt file) 212, 216
BC1339 BC1339 hypothetical protein (NCBI ptt file) 216, 284
BC1680 BC1680 Transcriptional regulator, XRE family (NCBI ptt file) 1, 337
BC1782 BC1782 hypothetical protein (NCBI ptt file) 216, 264
BC1958 BC1958 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file) 216, 284
BC2009 BC2009 hypothetical protein (NCBI ptt file) 1, 438
BC2147 BC2147 Response regulator aspartate phosphatase (NCBI ptt file) 216, 264
BC2148 BC2148 Response regulator aspartate phosphatase inhibitor (NCBI ptt file) 216, 264
BC2179 BC2179 Acetyltransferase (NCBI ptt file) 216, 224
BC2242 BC2242 hypothetical Cytosolic Protein (NCBI ptt file) 216, 227
BC2891 BC2891 SAM-dependent methyltransferase (NCBI ptt file) 216, 491
BC3247 BC3247 None 216, 294
BC3343 BC3343 Integral membrane protein (NCBI ptt file) 216, 414
BC3389 BC3389 Transcriptional regulator, MarR family (NCBI ptt file) 1, 74
BC3599 BC3599 Succinyl-CoA synthetase, alpha subunit-related enzymes (NCBI ptt file) 1, 51
BC3616 BC3616 Aconitate hydratase (NCBI ptt file) 1, 475
BC4001 BC4001 Transcriptional repressor PadR (NCBI ptt file) 1, 233
BC4106 BC4106 Alpha/beta hydrolase (NCBI ptt file) 1, 438
BC4259 BC4259 hypothetical Membrane Spanning Protein (NCBI ptt file) 1, 166
BC4380 BC4380 hypothetical Cytosolic Protein (NCBI ptt file) 216, 475
BC4483 BC4483 hypothetical protein (NCBI ptt file) 216, 381
BC4558 BC4558 hypothetical Membrane Spanning Protein (NCBI ptt file) 216, 264
BC4578 BC4578 hypothetical protein (NCBI ptt file) 216, 264
BC4613 BC4613 Metal-dependent hydrolase (NCBI ptt file) 203, 216
BC4631 BC4631 hypothetical protein (NCBI ptt file) 1, 438
BC4676 BC4676 hypothetical Cytosolic Protein (NCBI ptt file) 216, 264
BC4677 BC4677 General stress protein (NCBI ptt file) 216, 264
BC4714 BC4714 CarD-like transcriptional regulator (NCBI ptt file) 1, 119
BC4776 BC4776 hypothetical protein (NCBI ptt file) 216, 422
BC4790 BC4790 hypothetical Cytosolic Protein (NCBI ptt file) 1, 438
BC4923 BC4923 hypothetical protein (NCBI ptt file) 216, 264
BC4935 BC4935 HESB protein (NCBI ptt file) 1, 119
BC4952 BC4952 NifU protein (NCBI ptt file) 1, 216
BC4973 BC4973 Lipoic acid synthetase (NCBI ptt file) 1, 118
BC5010 BC5010 Transcriptional regulator (NCBI ptt file) 126, 216
BC5045 BC5045 hypothetical protein (NCBI ptt file) 1, 284
BC5047 BC5047 IG hypothetical 16995 (NCBI ptt file) 1, 74
BC5048 BC5048 Ferritin (NCBI ptt file) 1, 337
BC5128 BC5128 SsrA-binding protein (NCBI ptt file) 1, 505
BC5142 BC5142 Glutaredoxin (NCBI ptt file) 1, 28
BC5143 BC5143 RNA polymerase sigma-54 factor rpoN (NCBI ptt file) 1, 28
BC5197 BC5197 Transcriptional regulator, MarR family (NCBI ptt file) 1, 119
BC5440 BC5440 Autolysin response regulator (NCBI ptt file) 216, 220
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 BC4952
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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