Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 105 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 105

There are 11 regulatory influences for Module 105

Regulator Table (11)
Regulator Name Type
RSP_3341 tf
RSP_0547 tf
RSP_3694 tf
RSP_1660 tf
RSP_0386 tf
RSP_1704 tf
RSP_0068 tf
RSP_2800 tf
RSP_2922 tf
RSP_2867 tf
RSP_1077 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
7930 2.20e-01 tttTtaTTGatt.aG
Loader icon
7931 4.50e+03 TAcaaaaagc.GGgagaTGCa
Loader icon
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 105 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Environmental Information Processing kegg category 1.27e-04 1.44e-03 9/32
Membrane Transport kegg subcategory 5.00e-06 1.01e-04 9/32
ABC transporters kegg pathway 2.00e-06 3.90e-05 9/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 1.97e-02 3.07e-02 16/32
Cell wall/membrane/envelope biogenesis cog subcategory 3.21e-02 4.86e-02 3/32
Amino acid transport and metabolism cog subcategory 4.02e-04 8.01e-04 9/32
Inorganic ion transport and metabolism cog subcategory 3.36e-03 5.67e-03 5/32
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 105

There are 32 genes in Module 105

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_1262 RSP_1262 CDS None chromosome 1 3029531 3030118 - response regulator receiver protein (NCBI) False
RSP_1450 RSP_1450 CDS None chromosome 1 32769 33563 + Inositol monophosphatase family protein (NCBI) False
RSP_1451 RSP_1451 CDS None chromosome 1 33636 35210 + ABC peptide/nickel/opine transporter, periplasmic substrate-binding protein (NCBI) False
RSP_1453 RSP_1453 CDS None chromosome 1 36269 37180 + ABC peptide/nickel/opine transporter, inner membrane subunit (NCBI) False
RSP_1454 RSP_1454 CDS None chromosome 1 37182 39035 + ABC peptide/nickel/opine transporter, fused ATPase subunits (NCBI) False
RSP_1455 RSP_1455 CDS None chromosome 1 39028 40302 + putative N-carbamoyl-beta-alanine amidohydrolase (NCBI) False
RSP_1456 RSP_1456 CDS None chromosome 1 40299 41243 + hypothetical protein (NCBI) False
RSP_1457 RSP_1457 CDS None chromosome 1 41240 42184 + putative choline kinase (NCBI) False
RSP_1876 RSP_1876 CDS None chromosome 1 474764 475294 - hypothetical protein (NCBI) False
RSP_2032 RSP_2032 CDS None chromosome 1 629873 630277 + putative hypothetical Gifsy-1 prophage protein (NCBI) False
RSP_2036 RSP_2036 CDS None chromosome 1 632521 632718 + putative ECF/RNA polymerase sigma factor protein (NCBI) False
RSP_2157 RSP_2157 CDS None chromosome 1 760210 761145 - ABC transporter, inner membrane subunit (NCBI) False
RSP_2315 RSP_2315 CDS None chromosome 1 937445 937750 + hypothetical protein (NCBI) False
RSP_2750 RSP_2750 CDS None chromosome 1 1401018 1401476 + hypothetical protein (NCBI) False
RSP_2751 RSP_2751 CDS None chromosome 1 1401473 1402648 + hypothetical protein (NCBI) False
RSP_2753 RSP_2753 CDS None chromosome 1 1402642 1403139 + hypothetical protein (NCBI) False
RSP_2754 RSP_2754 CDS None chromosome 1 1403476 1404069 + hypothetical protein (NCBI) False
RSP_3057 RSP_3057 CDS None chromosome 2 97408 98499 - ABC proline/glycine betaine transporter, ATPase subunit (NCBI) False
RSP_3058 RSP_3058 CDS None chromosome 2 98492 99403 - ABC proline/glycine betaine transporter, inner membrane subunit (NCBI) False
RSP_3059 RSP_3059 CDS None chromosome 2 99471 100472 - ABC proline/glycine betaine transporter, periplasmic substrate-binding protein (NCBI) False
RSP_3106 RSP_3106 CDS None chromosome 2 151439 152263 - Cation efflux transporter, CDF family (NCBI) False
RSP_3151 RSP_3151 CDS None chromosome 2 200091 201083 - ABC nitrate/sulfonate/bicarbonate transporter family, periplasmic substrate-binding protein (NCBI) False
RSP_3152 RSP_3152 CDS None chromosome 2 201083 202090 - ABC nitrate/sulfonate/bicarbonate transporter family, periplasmic substrate-binding protein (NCBI) False
RSP_3154 RSP_3154 CDS None chromosome 2 203143 203973 - ABC nitrate/sulfonate/bicarbonate transporter family, ATPase subunit (NCBI) False
RSP_3421 RSP_3421 CDS None chromosome 2 490128 490703 + hypothetical protein (NCBI) False
RSP_3574 hutH CDS None chromosome 2 668567 670138 - putative histidine ammonia-lyase (NCBI) False
RSP_3655 RSP_3655 CDS None chromosome 2 763763 764668 - Dihydrodipicolinate synthase/N-acetylneuraminate lyase (NCBI) False
RSP_3656 RSP_3656 CDS None chromosome 2 764787 766313 - NAD-dependent aldehyde dehydrogenases (NCBI) False
RSP_3658 hpcH CDS None chromosome 2 767008 767808 - putative 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (NCBI) False
RSP_3670 RSP_3670 CDS None chromosome 2 789169 790167 - putative oxidoreductase myo-inositol 2-dehydrogenase (NCBI) False
RSP_3676 RSP_3676 CDS None chromosome 2 795171 795896 - transcriptional regulator, GntR family (NCBI) True
RSP_3785 RSP_3785 CDS None chromosome 2 902636 903658 - putative bacteriophage-related protein (NCBI) 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 105

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

comments powered by Disqus
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.