Organism : Bacillus cereus ATCC14579 | Module List :
BC1062

3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) cog/ cog
3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity go/ molecular_function
metabolic process go/ biological_process
Fatty acid biosynthesis kegg/ kegg pathway
Biosynthesis of unsaturated fatty acids kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1062
(Mouseover regulator name to see its description)

BC1062 is regulated by 27 influences and regulates 0 modules.
Regulators for BC1062 (27)
Regulator Module Operator
BC0598 330 tf
BC1915 330 tf
BC2672 330 tf
BC2760 330 tf
BC2770 330 tf
BC2979 330 tf
BC3128 330 tf
BC3493 330 tf
BC4072 330 tf
BC4104 330 tf
BC5265 330 tf
BC0785 34 tf
BC1032 34 tf
BC1080 34 tf
BC2410 34 tf
BC2672 34 tf
BC2738 34 tf
BC2760 34 tf
BC2770 34 tf
BC2801 34 tf
BC2988 34 tf
BC3244 34 tf
BC4072 34 tf
BC4104 34 tf
BC4499 34 tf
BC4661 34 tf
BC5205 34 tf

Warning: BC1062 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
3990 4.70e+02 taatcTCtttttttt
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3991 5.40e+03 aaGgagGA
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4574 1.30e+01 CaCCtccT
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4575 1.40e+04 CTTcCATGCcG
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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 BC1062

BC1062 is enriched for 6 functions in 3 categories.
Module neighborhood information for BC1062

BC1062 has total of 32 gene neighbors in modules 34, 330
Gene neighbors (32)
Gene Common Name Description Module membership
BC0395 BC0395 Metal-dependent hydrolase (NCBI ptt file) 72, 330
BC0547 BC0547 Sensory box/GGDEF family protein (NCBI ptt file) 34, 238
BC1062 BC1062 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file) 34, 330
BC1071 BC1071 hypothetical protein (NCBI ptt file) 194, 330
BC1347 BC1347 hypothetical protein (NCBI ptt file) 54, 330
BC1396 BC1396 Branched-chain amino acid aminotransferase (NCBI ptt file) 137, 330
BC1466 BC1466 hypothetical protein (NCBI ptt file) 34, 488
BC1604 BC1604 hypothetical protein (NCBI ptt file) 25, 330
BC1748 BC1748 Aspartokinase (NCBI ptt file) 330, 397
BC1799 BC1799 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 34, 137
BC2142 BC2142 Stage V sporulation protein S (NCBI ptt file) 34, 137
BC2143 BC2143 hypothetical Cytosolic Protein (NCBI ptt file) 34, 362
BC2144 BC2144 5-methylcytosine-specific restriction enzyme A (NCBI ptt file) 34, 154
BC2571 BC2571 hypothetical protein (NCBI ptt file) 330, 398
BC2669 BC2669 ThiJ/PfpI family protein (NCBI ptt file) 330, 398
BC2672 BC2672 Methyltransferase (NCBI ptt file) 330, 395
BC2730 BC2730 2-haloalkanoic acid dehalogenase (NCBI ptt file) 34, 525
BC3158 BC3158 Pyrimidine Reductase (NCBI ptt file) 34, 212
BC3262 BC3262 hypothetical protein (NCBI ptt file) 34, 238
BC3455 BC3455 Amino acid permease (NCBI ptt file) 330, 488
BC3465 BC3465 Acetyltransferase (NCBI ptt file) 34, 336
BC3519 BC3519 Response regulator aspartate phosphatase inhibitor (NCBI ptt file) 330, 395
BC3533 BC3533 Vancomycin B-type resistance protein vanW (NCBI ptt file) 34, 377
BC3580 BC3580 hypothetical protein (NCBI ptt file) 330, 488
BC3590 BC3590 ABC transporter permease protein (NCBI ptt file) 330, 427
BC3591 BC3591 ABC transporter ATP-binding protein (NCBI ptt file) 330, 427
BC3954 BC3954 hypothetical protein (NCBI ptt file) 330, 375
BC4134 BC4134 Pyrroline-5-carboxylate reductase (NCBI ptt file) 34, 377
BC4244 BC4244 hypothetical protein (NCBI ptt file) 34, 160
BC4515 BC4515 Esterase (NCBI ptt file) 330, 488
BC4946 BC4946 hypothetical protein (NCBI ptt file) 63, 330
BC5116 BC5116 hypothetical protein (NCBI ptt file) 34, 248
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 BC1062
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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