Organism : Bacillus cereus ATCC14579 | Module List :
BC4101

Transcriptional regulator, copG family (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4101
(Mouseover regulator name to see its description)

BC4101 is regulated by 34 influences and regulates 14 modules.
Regulators for BC4101 (34)
Regulator Module Operator
BC0405 113 tf
BC0647 113 tf
BC1080 113 tf
BC2549 113 tf
BC2801 113 tf
BC3105 113 tf
BC3589 113 tf
BC3868 113 tf
BC3922 113 tf
BC4072 113 tf
BC4073 113 tf
BC4101 113 tf
BC5038 113 tf
BC5265 113 tf
BC5363 113 tf
BC5402 113 tf
BC0057 154 tf
BC0410 154 tf
BC0601 154 tf
BC1080 154 tf
BC2362 154 tf
BC2526 154 tf
BC2670 154 tf
BC2738 154 tf
BC2801 154 tf
BC2811 154 tf
BC2979 154 tf
BC3434 154 tf
BC3589 154 tf
BC4072 154 tf
BC4101 154 tf
BC4165 154 tf
BC5205 154 tf
BC5409 154 tf

Warning: BC4101 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
4142 2.40e+02 ctg.AggaGgG
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4143 1.50e+03 Tcaa.atAAaAaAg.
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4224 3.60e-02 AaaaAgGgGg
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4225 1.40e+04 GTGcGcaGcAGGTTC
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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 BC4101

BC4101 is enriched for 2 functions in 2 categories.
Enrichment Table (2)
Function System
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC4101

BC4101 has total of 38 gene neighbors in modules 113, 154
Gene neighbors (38)
Gene Common Name Description Module membership
BC0573 BC0573 Two component system histidine kinase (NCBI ptt file) 113, 314
BC1082 BC1082 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 29, 113
BC1244 BC1244 IG hypothetical 16680 (NCBI ptt file) 113, 377
BC1395 BC1395 hypothetical protein (NCBI ptt file) 154, 395
BC2100 BC2100 Methyltransferase (NCBI ptt file) 113, 208
BC2144 BC2144 5-methylcytosine-specific restriction enzyme A (NCBI ptt file) 34, 154
BC2229 BC2229 Azoreductase (NCBI ptt file) 113, 525
BC2253 BC2253 hypothetical Cytosolic Protein (NCBI ptt file) 85, 154
BC2331 BC2331 Inosine-uridine preferring nucleoside hydrolase (NCBI ptt file) 154, 238
BC2339 BC2339 Metal-dependent hydrolase (NCBI ptt file) 113, 377
BC2406 BC2406 Metal-dependent hydrolase (NCBI ptt file) 113, 427
BC2413 BC2413 Phage protein (NCBI ptt file) 150, 154
BC2502 BC2502 hypothetical protein (NCBI ptt file) 113, 375
BC2503 BC2503 S-Adenosylhomocysteine nucleosidase (NCBI ptt file) 113, 456
BC2504 BC2504 Acetyltransferase (NCBI ptt file) 113, 420
BC2602 BC2602 hypothetical protein (NCBI ptt file) 154, 407
BC2670 BC2670 Transcriptional regulator, DeoR family (NCBI ptt file) 154, 308
BC2684 BC2684 Spermine/spermidine acetyltransferase (NCBI ptt file) 113, 210
BC2685 BC2685 CutA1 divalent ion tolerance protein (NCBI ptt file) 113, 210
BC2781 BC2781 Probable short-chain type dehydrogenase/reductase vdlC (NCBI ptt file) 113, 154
BC2802 BC2802 IG hypothetical 16873 (NCBI ptt file) 113, 154
BC2803 BC2803 Ubiquinone/menaquinone biosynthesis methyltransferase UBIE (NCBI ptt file) 113, 395
BC2804 BC2804 hypothetical Cytosolic Protein (NCBI ptt file) 47, 154
BC2806 BC2806 Acetyltransferase (NCBI ptt file) 113, 375
BC2848 BC2848 Oligopeptide-binding protein oppA (NCBI ptt file) 154, 356
BC3034 BC3034 Cytosine deaminase (NCBI ptt file) 113, 395
BC3035 BC3035 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 113, 469
BC3051 BC3051 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 154, 395
BC3338 BC3338 hypothetical Membrane Spanning Protein (NCBI ptt file) 154, 395
BC3414 BC3414 hydrolase (NCBI ptt file) 113, 208
BC3504 BC3504 (S)-2-hydroxy-acid oxidase chain D (NCBI ptt file) 154, 163
BC3658 BC3658 hypothetical ATP-binding protein (NCBI ptt file) 154, 427
BC3660 BC3660 hypothetical protein (NCBI ptt file) 123, 154
BC3967 BC3967 hypothetical protein (NCBI ptt file) 154, 217
BC4034 BC4034 Nitrilase (NCBI ptt file) 23, 154
BC4101 BC4101 Transcriptional regulator, copG family (NCBI ptt file) 113, 154
BC4641 BC4641 hypothetical protein (NCBI ptt file) 154, 217
BC5095 BC5095 Transposase (NCBI ptt file) 98, 113
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 BC4101
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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