Organism : Bacillus cereus ATCC14579 | Module List :
BC3576

Spore germination protein SC (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
spore germination go/ biological_process
membrane go/ cellular_component
spore_ger_x_C tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3576
(Mouseover regulator name to see its description)

BC3576 is regulated by 21 influences and regulates 0 modules.
Regulators for BC3576 (21)
Regulator Module Operator
BC1059 130 tf
BC1531 130 tf
BC1710 130 tf
BC2469 130 tf
BC2517 130 tf
BC4029 130 tf
BC4222 130 tf
BC4336 130 tf
BC5197 130 tf
BC5483 130 tf
BC0566 80 tf
BC0742 80 tf
BC1059 80 tf
BC1329 80 tf
BC2469 80 tf
BC2517 80 tf
BC3588 80 tf
BC3904 80 tf
BC4336 80 tf
BC4930 80 tf
BC5251 80 tf

Warning: BC3576 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
4080 6.30e-14 CCCGATTGGTgAgggCTgATaAtc
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4081 2.70e-04 GATtaaAGttTcaCTttAc
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4176 1.80e-18 CCCGATTGGTGaggGCtgATA
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4177 2.90e-06 CccCCAccTAAcTTctTtGCtttc
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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 BC3576

BC3576 is enriched for 3 functions in 4 categories.
Enrichment Table (3)
Function System
spore germination go/ biological_process
membrane go/ cellular_component
spore_ger_x_C tigr/ tigrfam
Module neighborhood information for BC3576

BC3576 has total of 31 gene neighbors in modules 80, 130
Gene neighbors (31)
Gene Common Name Description Module membership
BC0841 BC0841 Glucokinase regulatory protein (NCBI ptt file) 80, 387
BC0843 BC0843 outer surface protein (NCBI ptt file) 80, 387
BC0853 BC0853 Quaternary ammonium compound-resistance protein (NCBI ptt file) 80, 498
BC0960 BC0960 hypothetical protein (NCBI ptt file) 46, 80
BC1032 BC1032 Transcriptional repressor (NCBI ptt file) 80, 456
BC1106 BC1106 hypothetical protein (NCBI ptt file) 80, 377
BC1203 BC1203 Cell division protein ftsW (NCBI ptt file) 130, 455
BC1334 BC1334 hypothetical Exported Protein (NCBI ptt file) 80, 498
BC1440 BC1440 hypothetical protein (NCBI ptt file) 80, 387
BC1708 BC1708 hypothetical protein (NCBI ptt file) 30, 130
BC1845 BC1845 hypothetical protein (NCBI ptt file) 80, 523
BC2129 BC2129 hypothetical protein (NCBI ptt file) 80, 267
BC2291 BC2291 Transporter, LysE family (NCBI ptt file) 130, 405
BC2297 BC2297 hypothetical protein (NCBI ptt file) 80, 291
BC2402 BC2402 Tetracycline resistance protein (NCBI ptt file) 130, 468
BC2654 BC2654 Cobalt transport protein cbiQ (NCBI ptt file) 130, 181
BC2949 BC2949 hypothetical Membrane Spanning Protein (NCBI ptt file) 130, 455
BC3206 BC3206 hypothetical protein (NCBI ptt file) 80, 130
BC3207 BC3207 Two-component protein Kinase (NCBI ptt file) 130, 509
BC3235 BC3235 Glucose/mannose transporter (NCBI ptt file) 130, 347
BC3511 BC3511 Hydroxyacylglutathione hydrolase (NCBI ptt file) 130, 435
BC3574 BC3574 Spore germination protein SA (NCBI ptt file) 80, 130
BC3575 BC3575 Spore germination protein SB (NCBI ptt file) 80, 130
BC3576 BC3576 Spore germination protein SC (NCBI ptt file) 80, 130
BC4190 BC4190 Stage III sporulation protein AD (NCBI ptt file) 130, 321
BC4373 BC4373 hypothetical protein (NCBI ptt file) 130, 449
BC4497 BC4497 Tetracycline resistence protein TETA(L)/TETK (NCBI ptt file) 80, 456
BC4783 BC4783 hydrolase (HAD superfamily) (NCBI ptt file) 130, 248
BC4927 BC4927 Cell surface protein (NCBI ptt file) 130, 506
BC4934 BC4934 hypothetical protein (NCBI ptt file) 80, 235
BC5161 BC5161 CAPG protein (NCBI ptt file) 130, 230
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 BC3576
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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