Organism : Clostridium acetobutylicum | Module List:
Module 154 Profile

GeneModule member RegulatorRegulator MotifMotif
Cytoscape Web
Network Help

A network view of the module is created using cytoscapeWeb and enables dynamic, interactive exploration of the module properties. In this view, module member genes, motifs, and regulatory influences are represented as peripheral nodes connected to core module node via edges.

Module members are green circles, regulators are red triangles and motifs are blue diamonds. Selection of a node gives access to detailed information in a pop-up window, which allows dragging and pinning to compare multiple selections. Selecting module members will show information about the selected gene such as name, species and fucntions. Motif selection will show motif logo image and e-values. Bicluster selction will show expression profile and summary statistics for the module.

GeneModule member RegulatorRegulator MotifMotif
Regulators for Module 154

There are 14 regulatory influences for Module 154

Regulator Table (14)
Regulator Name Type
CAC0144 tf
CAC3429 tf
CAC2242 tf
CAC3200 tf
CAC0284 tf
CAC2143 tf
CAC0929 tf
CAC3647 tf
CAC0189 tf
CAC0426 tf
CAC3695 tf
CAC2113 tf
CAC1430 tf
CAC3475 tf

Regulator Help

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type.

tf: Transcription factor

ef: Environmental factor

combiner: Combinatorial influence of a tf or an ef through logic gate. Table is sortable by clicking on the arrows next to column headers.

Motif information (de novo identified motifs for modules)

There are 2 motifs predicted.

Motif Table (2)
Motif Id e-value Consensus Motif Logo
6960 2.80e-06 gGagGtG
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6961 1.70e+02 TAtAagTaGgCAAA
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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

Regulon 154 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
DNA metabolism tigr mainrole 3.80e-05 9.30e-05 4/25
DNA replication, recombination, and repair tigr sub1role 2.40e-05 6.60e-05 4/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 4.57e-03 8.26e-03 9/25
Replication, recombination and repair cog subcategory 1.61e-03 3.06e-03 4/25
Defense mechanisms cog subcategory 2.19e-04 5.05e-04 4/25
General function prediction only cog subcategory 2.29e-02 3.74e-02 5/25
Functions Help

Biological networks contain sets of regulatory units called functional modules that together play a role in regulation of specific functional processes. Connections between different modules in the network can help identify regulatory relationships such as hierarchy and epistasis. In addition, associating functions with modules enables putative assignment of functions to hypothetical genes. It is therefore essential to identify functional enrichment of modules within the regulatory network.

Functional annotations from single sources are often either not available or not complete. Therefore, we integrated KEGG pathway, Gene Ontology, TIGRFam and COG information as references for functional enrichment analysis.

We use hypergeometric p-values to identify significant overlaps between co-regulated module members and genes assigned to a particular functional annotation category. P-values are corrected for multiple comparisons by using Benjamini-Hochberg correction and filtered for p-values ≤ 0.05.

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.

Members for Module 154

There are 25 genes in Module 154

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0144 sfsa CDS None chromosome 149489 150181 + Sugar fermentation-stimulation protein (NCBI ptt file) True
CAC0245 CAC0245 CDS None chromosome 276621 277337 + ABC transporter ATP-binding protein (NCBI ptt file) False
CAC0296 csfB CDS None chromosome 352628 352843 + Zn-finger containing protein, csfB B.subtilis homolog (NCBI ptt file) False
CAC0502 uvrB CDS None chromosome 575260 577260 + Excinuclease ABC subunit B (helicase subunit of the DNA excision repair complex) (NCBI ptt file) False
CAC0503 uvrA CDS None chromosome 577260 580079 + Excinuclease ABC subunit A (ATP-ase), (uvrA) (NCBI ptt file) False
CAC0513 CAC0513 CDS None chromosome 589897 590850 + Uncharacterized conserved protein, similar to B.subtilis yvcL (NCBI ptt file) False
CAC0524 CAC0524 CDS None chromosome 604412 605098 + Response regulator (CheY-like and HTH domains) (NCBI ptt file) False
CAC0526 CAC0526 CDS None chromosome 606157 606840 + ABC transporter, ATPase component (NCBI ptt file) False
CAC0527 CAC0527 CDS None chromosome 606837 609428 + Predicted permease, domain duplication (NCBI ptt file) False
CAC0717 CAC0717 CDS None chromosome 830993 832516 + Predicted membrane protein (NCBI ptt file) False
CAC0748 CAC0748 CDS None chromosome 871093 871818 + Nitroreductase family protein (NCBI ptt file) False
CAC0749 CAC0749 CDS None chromosome 871872 872774 + HD hydrolase superfamily protein (NCBI ptt file) False
CAC0786 CAC0786 CDS None chromosome 908715 909086 - Uncharacterized conserved protein, repeats (NCBI ptt file) False
CAC0787 CAC0787 CDS None chromosome 909154 909603 - Uncharacterized conserved protein, repeats (NCBI ptt file) False
CAC0905 CAC0905 CDS None chromosome 1036900 1037835 + Uncharacterized NAD(FAD)-dependent dehydrogenase (NCBI ptt file) False
CAC0906 CAC0906 CDS None chromosome 1037885 1039048 + Alanyl-tRNA synthetase related protein (NCBI ptt file) False
CAC1004 CAC1004 CDS None chromosome 1152777 1153760 + Predicted membrane protein (NCBI ptt file) False
CAC2607 CAC2607 CDS None chromosome 2710314 2711117 - Short-chain alcohol dehydrogenase family protein (NCBI ptt file) False
CAC2737 sbcD CDS None chromosome 2864860 2866086 - DNA repair exonuclease (NCBI ptt file) False
CAC2763 CAC2763 CDS None chromosome 2895875 2897590 - Membrane assosiated methyl-accepting chemotaxis protein with HAMP domain (NCBI ptt file) False
CAC2824 CAC2824 CDS None chromosome 2954604 2957084 - N-terminal HKD family nuclease fused to DNA/RNA helicases of superfamily II,conserved in Streptomyces (NCBI ptt file) False
CAC2825 CAC2825 CDS None chromosome 2957099 2957545 - Uncharacterized conserved protein, YQXD B.subtilis ortholog (NCBI ptt file) False
CAC2947 topB CDS None chromosome 3079332 3081518 - Topoisomerase B (NCBI ptt file) False
CAC3302 gerKC CDS None chromosome 3468045 3469196 + Spore germination protein GerKC, membrane protein (NCBI ptt file) False
CAC3330 CAC3330 CDS None chromosome 3501973 3503229 + Cytochrome P450 family protein, YBDT B.subtilis ortholog (NCBI ptt file) False

Genes Help

Gene member table shows all the genes included in the module. Listed attributes are;

  1. Name: Gene name or Locus tag
  2. Common Name: Gene short name
  3. Type: Type of the feature, usually CDS.
  4. Gene ID: Link to NCBI Gene ID
  5. Chromosome: Chromosome name from annotation file
  6. Start/End:Feature start and end coordinates
  7. Strand: strand of the gene
  8. Description: Description of the gene from annotation file
  9. TF: If the gene is a Transcription Factor or not.

If you are browsing the Network Portal by using Gaggle/Firegoose, firegoose plugin will capture the NameList of the gene members. Captured names can be saved into your Workspace by clicking on "Capture" in the firegoose toolbar or can be directly sent other desktop and web resources by using "Broadcast" option.

Comments for Module 154

Please add your comments for this module by using the form below. Your comments will be publicly available.

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Social Help

You can start a conversation about this module or join the existing discussion by adding your comments. In order to be able to add your comments you need to sign in by using any of the following services;Disqus, Google, Facebook or Twitter. For full compatibility with other network portal features, we recommend using your Google ID.

Help

What is a module?

Regulatory units (modules) in the Network Portal are based on the network inference algorithm used. For the current version, modules are based on cMonkey modules and Inferelator regulatory influences on these modules. More specifically, module refers to set of genes that are conditionally co-regulated under subset of the conditions. Identification of modules integrates co-expression, de-novo motif identification, and other functional associations such as operon information and protein-protein interactions.

Module Overview

The landing module page shows quick summary info including co-expression profiles, de-novo identified motifs, and transcription factors and/or environmental factors as regulatory influences. It also includes module residual, motif e-values, conditions and links to other resources such as NCBI and Microbesonline. . If a transcription factor is included in the manually curated RegPrecise database, further information from RegPrecise is shown, allowing users to perform comparative analysis.

Expression Profiles

Expression profiles is a plot of the expression ratios (log10) of the module's genes, over all subset of the conditions included in the module. The X-axis represent conditions and the Y-axis represents log10 expression ratios. Each gene is plotted as line plot with different colors. Colored legend for the lines are presented under the plot. This plot is dynamic. Clicking on the gene names in the legend will show/hide the plot for that particular gene. A tooltip will show expression ratio information if you mouseover the lines in the plot.

Motif Locations

Location of the Identified motifs for the module in the upstream regions of the member genes are shown under the expression profiles plot. This plot shows the diagram of the upstream positions of the motifs, colored red and green for motifs #1, and 2, respectively. Intensity of the color is proportional to the significance of the occurence of that motif at a given location. Motifs on the forward and reverse strand are represented over and under the line respectively.

Network

A network view of the module is created using cytoscapeWeb and enables dynamic, interactive exploration of the module properties. In this view, module member genes, motifs, and regulatory influences are represented as peripheral nodes connected to core module node via edges. Module members are green circles, regulators are red triangles and motifs are blue diamonds. Selection of a node gives access to detailed information in a pop-up window, which allows dragging and pinning to compare multiple selections. Selecting module members will show information about the selected gene such as name, species and fucntions. Motif selection will show motif logo image and e-values. Bicluster selction will show expression profile and summary statistics for the module.

GeneModule member RegulatorRegulator MotifMotif

Regulators

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type. tf: Transcription factor, ef: Environmental factor and combiner:Combinatorial influence of a tf or an ef through logic gate. Tabel is sortable by clicking on the arrows next to column headers.

Motifs

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.

Functions

Biological networks contain sets of regulatory units called functional modules that together play a role in regulation of specific functional processes. Connections between different modules in the network can help identify regulatory relationships such as hierarchy and epistasis. In addition, associating functions with modules enables putative assignment of functions to hypothetical genes. It is therefore essential to identify functional enrichment of modules within the regulatory network.

Functional annotations from single sources are often either not available or not complete. Therefore, we integrated KEGG pathway, Gene Ontology, TIGRFam and COG information as references for functional enrichment analysis.

We use hypergeometric p-values to identify significant overlaps between co-regulated module members and genes assigned to a particular functional annotation category. P-values are corrected for multiple comparisons by using Benjamini-Hochberg correction and filtered for p-values ≤ 0.05.

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.

Genes

Gene member table shows all the genes included in the module. Listed attributes are;

  1. Name: Gene name or Locus tag
  2. Common Name: Gene short name
  3. Type: Type of the feature, usually CDS.
  4. Gene ID: Link to NCBI Gene ID
  5. Chromosome: Chromosome name from annotation file
  6. Start/End:Feature start and end coordinates
  7. Strand: strand of the gene
  8. Description: Description of the gene from annotation file
  9. TF: If the gene is a Transcription Factor or not.

If you are browsing the Network Portal by using Gaggle/Firegoose, firegoose plugin will capture the NameList of the gene members. Captured names can be saved into your Workspace by clicking on "Capture" in the firegoose toolbar or can be directly sent other desktop and web resources by using "Broadcast" option.

Social

You can start a conversation about this module or join the existing discussion by adding your comments. In order to be able to add your comments you need to sign in by using any of the following services;Disqus, Google, Facebook or Twitter. For full compatibility with other network portal features, we recommend using your Google ID.

Definitions

Residual: is a measure of bicluster quality. Mean bicluster residual is smaller when the expression profile of the genes in the module is "tighter". So smaller residuals are usually indicative of better bicluster quality.

Expression Profile: is a preview of the expression profiles of all the genes under subset of conditions included in the module. Tighter expression profiles are usually indicative of better bicluster quality.

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.

Genes: Number of genes included in the module.

Functions: We identify functional enrichment of each module by camparing to different functional categories such as KEGG, COG, GO etc. by using hypergeometric function. If the module is significantly enriched for any of the functions, this column will list few of the these functions as an overview. Full list of functions is available upon visiting the module page under the Functions tab.