Organism : Halobacterium salinarum NRC-1 | Module List:
Module 2 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 2

There are 8 regulatory influences for Module 2

Regulator Table (8)
Regulator Name Type
VNG1836G tf
VNG0194H tf
VNG0258H tf
VNG2243G tf
VNG2661G
VNG1123G
combiner
VNG2661G
VNG1029C
combiner
VNG0040C tf
VNG0101G
VNG2163H
combiner

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
983 6.60e+00 aAaaTcAAAacctaTaA.T
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984 1.10e+03 a.gaac.ccGcaAc.accttga.g
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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 2 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Citrate cycle (TCA cycle) kegg pathway 2.21e-04 1.38e-03 3/31
Butanoate metabolism kegg pathway 2.50e-05 2.70e-04 3/31
Oxidative phosphorylation kegg pathway 0.00e+00 0.00e+00 10/31
Carbon fixation pathways in prokaryotes kegg pathway 3.91e-04 1.99e-03 3/31
Methane metabolism kegg pathway 2.60e-05 2.83e-04 4/31
Metabolic pathways kegg pathway 3.05e-03 7.84e-03 10/31
Microbial metabolism in diverse environments kegg pathway 2.99e-02 4.31e-02 3/31
Carbohydrate Metabolism kegg subcategory 3.01e-03 1.21e-02 6/31
Energy Metabolism kegg subcategory 0.00e+00 0.00e+00 17/31
Metabolism kegg subcategory 2.91e-04 1.88e-03 16/31
Metabolism kegg category 0.00e+00 0.00e+00 25/31
Global kegg category 2.91e-04 1.71e-03 16/31
Metabolism kegg category 4.44e-04 2.68e-03 12/31
Carbohydrate Metabolism kegg subcategory 2.06e-02 4.21e-02 3/31
Citrate cycle (TCA cycle) kegg pathway 2.21e-04 1.63e-03 3/31
Butanoate metabolism kegg pathway 2.50e-05 2.80e-04 3/31
Energy Metabolism kegg subcategory 0.00e+00 0.00e+00 11/31
Oxidative phosphorylation kegg pathway 0.00e+00 0.00e+00 10/31
Carbon fixation pathways in prokaryotes kegg pathway 3.91e-04 2.45e-03 3/31
Methane metabolism kegg pathway 2.60e-05 2.96e-04 4/31
Global kegg category 3.94e-03 1.24e-02 10/31
Metabolism kegg subcategory 3.94e-03 1.24e-02 10/31
Metabolic pathways kegg pathway 3.05e-03 1.04e-02 10/31

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 6.11e-04 1.53e-03 5/31
cellular component movement biological_process 2.00e-06 1.20e-05 3/31
ATP synthesis coupled proton transport biological_process 1.10e-05 6.00e-05 3/31
succinate dehydrogenase activity molecular_function 0.00e+00 0.00e+00 3/31
GTPase activity molecular_function 7.00e-06 2.80e-05 3/31
hydrogen-transporting two-sector ATPase activity molecular_function 7.00e-06 2.80e-05 3/31
structural molecule activity molecular_function 1.70e-05 6.50e-05 3/31
GTP binding molecular_function 2.70e-04 6.58e-04 3/31
NADH dehydrogenase (ubiquinone) activity molecular_function 0.00e+00 2.00e-06 4/31
hydrogen ion transporting ATP synthase activity, rotational mechanism molecular_function 1.70e-05 6.50e-05 3/31
proton-transporting ATPase activity, rotational mechanism molecular_function 1.70e-05 6.50e-05 3/31

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 1.61e-03 7.10e-03 3/31
Energy metabolism tigr mainrole 1.61e-03 2.40e-03 3/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Archaeal flagellins cog 1.00e-06 1.00e-06 3/31
Cell motility cog subcategory 1.61e-03 1.68e-02 3/31
Posttranslational modification, protein turnover, chaperones cog subcategory 3.39e-04 5.65e-03 5/31
Energy production and conversion cog subcategory 2.00e-06 6.40e-05 9/31
Cellular processes and signaling cog category 6.81e-04 1.04e-02 10/31
Cellular processes and signaling cog category 1.03e-03 1.93e-03 9/31
Cell motility cog subcategory 1.61e-03 2.92e-03 3/31
Posttranslational modification, protein turnover, chaperones cog subcategory 3.39e-04 6.84e-04 5/31
Energy production and conversion cog subcategory 2.00e-06 5.00e-06 9/31
Archaeal flagellins cog 1.00e-06 2.00e-06 3/31
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 2

There are 31 genes in Module 2

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
VNG0013C CDS 1446959 chromosome 11478 12614 - hypothetical protein VNG0013C False
VNG0166G psmB CDS 1447092 chromosome 142335 143096 + proteasome subunit alpha False
VNG0192G ftsZ2 CDS 1447112 chromosome 165152 166279 - cell division protein FtsZ False
VNG0207H CDS 1447124 chromosome 175115 175471 + hypothetical protein VNG0207H False
VNG0208H CDS 1447125 chromosome 175471 175920 + hypothetical protein VNG0208H False
VNG0209H CDS 1447126 chromosome 175913 176947 + hypothetical protein VNG0209H False
VNG0234C CDS 1447146 chromosome 196288 196665 - hypothetical protein VNG0234C False
VNG0524G yurY CDS 1447354 chromosome 404888 405814 + ABC transporter ATP-binding protein False
VNG0527C CDS 1447356 chromosome 407277 408491 + hypothetical protein VNG0527C False
VNG0584H CDS 1447401 chromosome 447481 448311 - hypothetical protein VNG0584H False
VNG0585H CDS 1447402 chromosome 448314 448700 - hypothetical protein VNG0585H False
VNG0620G edp CDS 1447431 chromosome 472598 473500 - proteinase IV-like protein False
VNG0635G nolB CDS 1447443 chromosome 485194 485604 + NADH dehydrogenase/oxidoreductase-like protein False
VNG0637G ndhG5 CDS 1447445 chromosome 486301 487989 + NADH dehydrogenase/oxidoreductase False
VNG0640G nolD CDS 1447447 chromosome 489042 489503 + NADH dehydrogenase/oxidoreductase-like protein False
VNG0642C CDS 1447449 chromosome 489893 490126 + hypothetical protein VNG0642C False
VNG0960G flaB1 CDS 1447685 chromosome 731799 732380 + flagellin B1 False
VNG0961G flaB2 CDS 1447686 chromosome 732464 732982 + flagellin B2 False
VNG0962G flaB3 CDS 1447687 chromosome 733066 733575 + flagellin B3 False
VNG1149Cm CDS 1449038 chromosome 869155 870501 + metallo-beta-lactamase superfamily hydrolase False
VNG1306G sdhA CDS 1447950 chromosome 976559 978406 - hypothetical protein VNG1306G False
VNG1308G sdhB CDS 1447951 chromosome 978413 979291 - hypothetical protein VNG1308G False
VNG1310G sdhC CDS 1447953 chromosome 979662 980084 - hypothetical protein VNG1310G False
VNG2135G atpD CDS 1448576 chromosome 1569547 1570221 - V-type ATP synthase subunit D False
VNG2143G atpK CDS 1448584 chromosome 1577503 1577718 - H+-transporting ATP synthase subunit K False
VNG2146H CDS 1448586 chromosome 1579939 1580271 - hypothetical protein VNG2146H False
VNG2648G rps10p CDS 1448988 chromosome 1984401 1984709 - 30S ribosomal protein S10P False
VNG2649G eef1a CDS 1448989 chromosome 1984713 1985978 - elongation factor 1-alpha False
VNG2654Gm EEF2 CDS 1449076 chromosome 1989693 1991879 - elongation factor EF-2 False
VNG2666G rpoB'' CDS 1448999 chromosome 2000487 2002058 - DNA-directed RNA polymerase subunit beta'' False
VNG6313G nhaC3 CDS 1449193 pNRC200 242960 244417 - Na+/H+ antiporter 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 2

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.