Organism : Bacillus cereus ATCC14579 | Module List :
BC3976

putative transcriptional regulator (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
Uncharacterized conserved small protein cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3976
(Mouseover regulator name to see its description)

BC3976 is regulated by 22 influences and regulates 29 modules.
Regulators for BC3976 (22)
Regulator Module Operator
BC0051 371 tf
BC0116 371 tf
BC0158 371 tf
BC1531 371 tf
BC3128 371 tf
BC3332 371 tf
BC3814 371 tf
BC3976 371 tf
BC4181 371 tf
BC4294 371 tf
BC4570 371 tf
BC4603 371 tf
BC4670 371 tf
BC0051 326 tf
BC0116 326 tf
BC3976 326 tf
BC4170 326 tf
BC4289 326 tf
BC4670 326 tf
BC4672 326 tf
BC5339 326 tf
BC5463 326 tf

Warning: BC3976 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
4566 2.00e-02 ccCTCC
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4567 1.20e+04 GCTcgtCaTAc
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4652 7.70e+01 GaAGgGg
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4653 1.10e+00 AGcAaaAAggAggg
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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 BC3976

BC3976 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Uncharacterized conserved small protein cog/ cog
Module neighborhood information for BC3976

BC3976 has total of 32 gene neighbors in modules 326, 371
Gene neighbors (32)
Gene Common Name Description Module membership
BC0084 BC0084 Lysyl-tRNA synthetase (NCBI ptt file) 326, 471
BC0445 BC0445 TerC-like protein (NCBI ptt file) 169, 326
BC0779 BC0779 Thiol-disulfide oxdoreductase BdbC (NCBI ptt file) 300, 326
BC1483 BC1483 Ferredoxin (NCBI ptt file) 169, 326
BC3774 BC3774 Pyruvate synthase alpha chain (NCBI ptt file) 371, 455
BC3793 BC3793 Cell division protein ftsK (NCBI ptt file) 371, 390
BC3797 BC3797 Dihydrodipicolinate synthase (NCBI ptt file) 371, 474
BC3798 BC3798 Aspartokinase (NCBI ptt file) 371, 426
BC3799 BC3799 Aspartate-semialdehyde dehydrogenase (NCBI ptt file) 371, 426
BC3807 BC3807 Riboflavin kinase (NCBI ptt file) 71, 371
BC3808 BC3808 tRNA pseudouridine synthase B (NCBI ptt file) 71, 371
BC3854 BC3854 Predicted kinase related to hydroxyacetone kinase (NCBI ptt file) 260, 371
BC3855 BC3855 putative alkaline-shock protein (NCBI ptt file) 371, 447
BC3960 BC3960 hypothetical protein (NCBI ptt file) 270, 326
BC3976 BC3976 putative transcriptional regulator (NCBI ptt file) 326, 371
BC4051 BC4051 Transcription antiterminator, BglG family (NCBI ptt file) 270, 326
BC4180 BC4180 Methylenetetrahydrofolate dehydrogenase (NADP+) (NCBI ptt file) 371, 450
BC4278 BC4278 High-affinity zinc uptake system membrane protein znuB (NCBI ptt file) 169, 371
BC4280 BC4280 hypothetical Membrane Spanning Protein (NCBI ptt file) 169, 326
BC4289 BC4289 RNA polymerase sigma factor rpoD (NCBI ptt file) 269, 326
BC4292 BC4292 EMG2 protein (NCBI ptt file) 371, 447
BC4293 BC4293 hypothetical Cytosolic Protein (NCBI ptt file) 371, 455
BC4294 BC4294 CBS domain containing protein (NCBI ptt file) 371, 455
BC4297 BC4297 GTP-binding protein (NCBI ptt file) 273, 371
BC4298 BC4298 Cytidine deaminase (NCBI ptt file) 71, 371
BC4853 BC4853 Naphthoate synthase (NCBI ptt file) 326, 471
BC4898 BC4898 Glucose-6-phosphate isomerase (NCBI ptt file) 270, 326
BC4918 BC4918 UTP--glucose-1-phosphate uridylyltransferase (NCBI ptt file) 326, 372
BC4919 BC4919 Phosphoglucomutase (NCBI ptt file) 169, 326
BC4969 BC4969 hypothetical Membrane Spanning Protein (NCBI ptt file) 166, 326
BC5043 BC5043 Sodium/proton-dependent alanine carrier protein (NCBI ptt file) 169, 326
BC5335 BC5335 Fructose-bisphosphate aldolase (NCBI ptt file) 169, 326
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 BC3976
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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