Organism : Bacillus cereus ATCC14579 | Module List :
BC0601

Transcriptional activator NprR (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0601
(Mouseover regulator name to see its description)

BC0601 is regulated by 34 influences and regulates 11 modules.
Regulators for BC0601 (34)
Regulator Module Operator
BC0114 73 tf
BC0598 73 tf
BC0601 73 tf
BC0613 73 tf
BC0648 73 tf
BC1003 73 tf
BC1884 73 tf
BC2217 73 tf
BC2340 73 tf
BC2362 73 tf
BC2632 73 tf
BC3493 73 tf
BC3982 73 tf
BC4104 73 tf
BC4652 73 tf
BC0601 47 tf
BC0648 47 tf
BC0758 47 tf
BC0785 47 tf
BC0954 47 tf
BC0993 47 tf
BC1915 47 tf
BC2340 47 tf
BC2738 47 tf
BC2801 47 tf
BC3072 47 tf
BC3163 47 tf
BC3244 47 tf
BC3405 47 tf
BC3438 47 tf
BC3891 47 tf
BC4072 47 tf
BC4206 47 tf
BC5265 47 tf

Warning: BC0601 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
4014 8.00e-02 TCcTttt.TaT
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4015 8.10e+00 AGgAGG
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4066 7.90e-02 GAgGtG
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4067 6.90e+01 TaTTTtttCttTttTctAacaaA
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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 BC0601

BC0601 is enriched for 1 functions in 2 categories.
Enrichment Table (1)
Function System
binding go/ molecular_function
Module neighborhood information for BC0601

BC0601 has total of 53 gene neighbors in modules 47, 73
Gene neighbors (53)
Gene Common Name Description Module membership
BC0344 BC0344 Delta-1-pyrroline-5-carboxylate dehydrogenase (NCBI ptt file) 73, 488
BC0483 BC0483 Penicillin-binding protein (NCBI ptt file) 47, 299
BC0598 BC0598 Transcriptional activator NprR (NCBI ptt file) 73, 488
BC0601 BC0601 Transcriptional activator NprR (NCBI ptt file) 47, 73
BC0686 BC0686 hypothetical protein (NCBI ptt file) 47, 409
BC0758 BC0758 Transcriptional regulator, MarR family (NCBI ptt file) 47, 286
BC0901 BC0901 Deblocking aminopeptidase (NCBI ptt file) 47, 194
BC1178 BC1178 hypothetical protein (NCBI ptt file) 20, 73
BC1275 BC1275 Methyltransferase (NCBI ptt file) 47, 286
BC1312 BC1312 3-hydroxybutyryl-CoA dehydratase (NCBI ptt file) 73, 120
BC1313 BC1313 PhaP protein (NCBI ptt file) 73, 120
BC1314 BC1314 PhaQ protein (NCBI ptt file) 73, 120
BC1315 BC1315 PhaQ protein (NCBI ptt file) 73, 120
BC1316 BC1316 PhaR protein (NCBI ptt file) 73, 120
BC1317 BC1317 Acetoacetyl-CoA reductase (NCBI ptt file) 73, 120
BC1318 BC1318 Poly-beta-hydroxybutyrate polymerase (NCBI ptt file) 73, 120
BC1348 BC1348 hypothetical protein (NCBI ptt file) 73, 409
BC1726 BC1726 hypothetical Membrane Spanning Protein (NCBI ptt file) 47, 194
BC1994 BC1994 NH(3)-dependent NAD(+) synthetase (NCBI ptt file) 47, 77
BC2311 BC2311 4'-phosphopantetheinyl transferase (NCBI ptt file) 47, 77
BC2312 BC2312 hypothetical protein (NCBI ptt file) 47, 77
BC2632 BC2632 Transcriptional regulator, AraC family (NCBI ptt file) 73, 434
BC2661 BC2661 Bacitracin transport permease protein BCRC (NCBI ptt file) 47, 77
BC2664 BC2664 Penicillin-binding protein (NCBI ptt file) 73, 520
BC2679 BC2679 hypothetical protein (NCBI ptt file) 47, 299
BC2686 BC2686 MutT/nudix family protein (NCBI ptt file) 47, 427
BC2714 BC2714 Acetyltransferase (NCBI ptt file) 47, 409
BC2804 BC2804 hypothetical Cytosolic Protein (NCBI ptt file) 47, 154
BC2807 BC2807 hypothetical protein (NCBI ptt file) 47, 258
BC2808 BC2808 hypothetical Membrane Spanning Protein (NCBI ptt file) 47, 258
BC2896 BC2896 Aspartate aminotransferase (NCBI ptt file) 73, 488
BC2897 BC2897 (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase (NCBI ptt file) 73, 488
BC2898 BC2898 Pantothenate kinase (NCBI ptt file) 73, 488
BC3037 BC3037 Mutator mutT protein (7,8-dihydro-8-oxoguanine-triphosphatase) (NCBI ptt file) 47, 299
BC3070 BC3070 Signal peptidase I (NCBI ptt file) 47, 480
BC3071 BC3071 Copper homeostasis protein cutC (NCBI ptt file) 43, 47
BC3072 BC3072 Transcriptional regulator, ArsR family (NCBI ptt file) 47, 449
BC3073 BC3073 hypothetical protein (NCBI ptt file) 47, 480
BC3143 BC3143 hypothetical Cytosolic Protein (NCBI ptt file) 47, 511
BC3144 BC3144 hypothetical Cytosolic Protein (NCBI ptt file) 47, 511
BC3635 BC3635 hypothetical protein (NCBI ptt file) 47, 175
BC3727 BC3727 Formate transporter (NCBI ptt file) 47, 286
BC4125 BC4125 hypothetical protein (NCBI ptt file) 47, 445
BC4340 BC4340 NAD(P)H nitroreductase (NCBI ptt file) 47, 286
BC4427 BC4427 Prephenate dehydratase (NCBI ptt file) 73, 137
BC4897 BC4897 IG hypothetical 16740 (NCBI ptt file) 47, 491
BC4938 BC4938 NADH dehydrogenase (NCBI ptt file) 73, 434
BC4971 BC4971 Phosphoglycerate mutase (NCBI ptt file) 73, 422
BC4972 BC4972 DNA-binding protein (NCBI ptt file) 73, 422
BC5076 BC5076 Short chain dehydrogenase (NCBI ptt file) 73, 137
BC5077 BC5077 hypothetical protein (NCBI ptt file) 73, 137
BC5091 BC5091 SnoK-like protein (NCBI ptt file) 73, 120
BC5092 BC5092 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily (NCBI ptt file) 73, 120
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 BC0601
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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