Organism : Bacillus cereus ATCC14579 | Module List :
BC0365

Nitrogen regulation protein NIFR3 (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
tRNA-dihydrouridine synthase cog/ cog
tRNA processing go/ biological_process
oxidoreductase activity go/ molecular_function
flavin adenine dinucleotide binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0365
(Mouseover regulator name to see its description)

BC0365 is regulated by 32 influences and regulates 0 modules.
Regulators for BC0365 (32)
Regulator Module Operator
BC0230 399 tf
BC0607 399 tf
BC1363 399 tf
BC2218 399 tf
BC2672 399 tf
BC3084 399 tf
BC3332 399 tf
BC3792 399 tf
BC3814 399 tf
BC3826 399 tf
BC3868 399 tf
BC4356 399 tf
BC4525 399 tf
BC4842 399 tf
BC5024 399 tf
BC0116 432 tf
BC0122 432 tf
BC0518 432 tf
BC0598 432 tf
BC0607 432 tf
BC0954 432 tf
BC1337 432 tf
BC2362 432 tf
BC2672 432 tf
BC2770 432 tf
BC3062 432 tf
BC3400 432 tf
BC3826 432 tf
BC3982 432 tf
BC4010 432 tf
BC4057 432 tf
BC4499 432 tf

Warning: BC0365 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
4708 2.80e+04 CcCGTTCTAatGCc
Loader icon
4709 5.00e+02 tAaggagGaa
Loader icon
4774 3.80e+00 Aa.aGaGG.at
Loader icon
4775 8.50e+03 CGGcCcc
Loader icon
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 BC0365

BC0365 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
tRNA-dihydrouridine synthase cog/ cog
tRNA processing go/ biological_process
oxidoreductase activity go/ molecular_function
flavin adenine dinucleotide binding go/ molecular_function
Module neighborhood information for BC0365

BC0365 has total of 39 gene neighbors in modules 399, 432
Gene neighbors (39)
Gene Common Name Description Module membership
BC0190 BC0190 Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] (NCBI ptt file) 134, 399
BC0303 BC0303 Alpha/beta hydrolase (NCBI ptt file) 10, 432
BC0365 BC0365 Nitrogen regulation protein NIFR3 (NCBI ptt file) 399, 432
BC0607 BC0607 Transcriptional regulator, LytR family (NCBI ptt file) 159, 432
BC0813 BC0813 enterotoxin / cell-wall binding protein (NCBI ptt file) 399, 482
BC0892 BC0892 hypothetical protein (NCBI ptt file) 399, 477
BC0902 BC0902 S-layer protein / N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 425, 432
BC1231 BC1231 Sodium/proline symporter (NCBI ptt file) 139, 399
BC1247 BC1247 hypothetical protein (NCBI ptt file) 92, 432
BC1337 BC1337 Transcriptional regulator, MarR family (NCBI ptt file) 432, 479
BC2185 BC2185 Protein ecsB (NCBI ptt file) 341, 432
BC2234 BC2234 Arginine/ornithine antiporter (NCBI ptt file) 159, 399
BC2391 BC2391 hypothetical protein (NCBI ptt file) 388, 432
BC2554 BC2554 hypothetical protein (NCBI ptt file) 257, 432
BC2704 BC2704 Serine protease (NCBI ptt file) 432, 460
BC2887 BC2887 hypothetical Cytosolic Protein (NCBI ptt file) 399, 465
BC2929 BC2929 Peptidoglycan N-acetylglucosamine deacetylase (NCBI ptt file) 382, 399
BC3084 BC3084 Transcriptional regulator, TetR family (NCBI ptt file) 249, 399
BC3094 BC3094 L-asparaginase (NCBI ptt file) 161, 399
BC3708 BC3708 GTP-binding protein hflX (NCBI ptt file) 176, 432
BC3772 BC3772 tRNA 2-methylthioadenosine synthase (NCBI ptt file) 243, 399
BC3831 BC3831 DNA topoisomerase I (NCBI ptt file) 192, 399
BC3981 BC3981 Tetrahydrodipicolinate N-acetyltransferase (NCBI ptt file) 103, 399
BC4010 BC4010 Transcriptional regulator, LacI family (NCBI ptt file) 139, 432
BC4300 BC4300 hypothetical Metal-Binding Protein (NCBI ptt file) 27, 399
BC4301 BC4301 Metal-dependent phosphohydrolase (NCBI ptt file) 27, 399
BC4499 BC4499 Transcriptional regulator, TetR family (NCBI ptt file) 75, 432
BC4653 BC4653 GAF domain-containing proteins (NCBI ptt file) 399, 505
BC4706 BC4706 NAD(FAD)-utilizing dehydrogenases (NCBI ptt file) 399, 433
BC4722 BC4722 Molybdenum cofactor biosynthesis protein C (NCBI ptt file) 74, 399
BC5026 BC5026 hypothetical protein (NCBI ptt file) 67, 432
BC5027 BC5027 Protein erfK/srfK precursor (NCBI ptt file) 67, 432
BC5063 BC5063 UDP-N-acetylenolpyruvoylglucosamine reductase (NCBI ptt file) 37, 432
BC5185 BC5185 Cell division protein ftsX (NCBI ptt file) 37, 399
BC5239 BC5239 enterotoxin / cell-wall binding protein (NCBI ptt file) 399, 465
BC5289 BC5289 hypothetical protein (NCBI ptt file) 319, 432
BC5290 BC5290 hypothetical protein (NCBI ptt file) 319, 432
BC5371 BC5371 Spermidine synthase (NCBI ptt file) 399, 479
BC5407 BC5407 Chloride channel protein (NCBI ptt file) 67, 432
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 BC0365
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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