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Module #509, TG: 3, TC: 2, 61 probes, 61 Entrez genes, 5 conditions
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The image plot shows the color-coded level of gene expression, for the
genes and conditions in a given transcription module. The genes are on
the horizontal, the conditions on the vertical axis.
The genes are ordered according to their ISA gene scores, similarly
the conditions are ordered according to their condition scores. The
score of a gene means the «degree of inclusion» in
the module: a high score gene is essential in the module.
Condition scores can also be negative, that means that the genes of
the module are all down-regulated in the condition. Here the absolute
value of the score gives the «degree of inclusion».
The plots above and beside the expression matrix show the gene scores
and condition scores, respectively.
Note that the plot is interactive, you can see the name of the gene
and condition under the mouse cursor.
The expression matrix was normalized to have mean zero and standard
deviation one for every gene separately across all conditions
(i.e. not just for the conditions in the module).
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Under-expression is coded with green,
over-expression with red color.
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The GO tree — Biological processes
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This is one of three sections showing Gene Ontology enrichment of the
current module: in this case for biological processes.
The graph shows the hierarchy of the GO categories, their enrichment
for the current module is color coded, and the blue number beside the
category is the minus log ten p-value of the enrichment. (Calculated
using the standard hypergeometric test.) The color of the arrows code
«is a» (cyan) and «part of» relationships.
The tree was built the following way. First all GO terms with more
significant enrichment p-value than 0.05 were collected. Then all
paths from these terms to the root node of the GO tree were included
too. If a GO term is included more than once in the tree, then the
green numbers show 1) the id of the node, this makes it easier to find
other appereances of the term, and 2) the number of appearences.
Note that the same GO category might show up on the graph many
times. This is because the GO was «straightened» for this
graph, i.e. if there are more paths from a GO term to the root node of
the tree, all of them are included. The green numbers
Move the mouse cursor over the terms to get their definition. Clicking
on them takes you to the corresponding Gene Ontology web page.
If you cannot see a graph here at all, that means that there were no
significantly enriched GO categories, at the 0.05 level.
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metabolic process
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
xenobiotic metabolic process
The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
biological_process
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
response to xenobiotic stimulus
A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a xenobiotic compound stimulus. Xenobiotic compounds are compounds foreign to living organisms.
cellular process
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
response to chemical stimulus
A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
cellular metabolic process
The chemical reactions and pathways by which individual cells transform chemical substances.
response to stimulus
A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
all
This term is the most general term possible
cellular metabolic process
The chemical reactions and pathways by which individual cells transform chemical substances.
xenobiotic metabolic process
The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
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The GO tree — Cellular Components
HELP
This is one of three sections showing Gene Ontology enrichment of the
current module: in this case for cellular components.
The graph shows the hierarchy of the GO categories, their enrichment
for the current module is color coded, and the blue number beside the
category is the minus log ten p-value of the enrichment. (Calculated
using the standard hypergeometric test.) The color of the arrows code
«is a» (cyan) and «part of» relationships.
The tree was built the following way. First all GO terms with more
significant enrichment p-value than 0.05 were collected. Then all
paths from these terms to the root node of the GO tree were included
too. If a GO term is included more than once in the tree, then the
green numbers show 1) the id of the node, this makes it easier to find
other appereances of the term, and 2) the number of appearences.
Note that the same GO category might show up on the graph many
times. This is because the GO was «straightened» for this
graph, i.e. if there are more paths from a GO term to the root node of
the tree, all of them are included. The green numbers
Move the mouse cursor over the terms to get their definition. Clicking
on them takes you to the corresponding Gene Ontology web page.
If you cannot see a graph here at all, that means that there were no
significantly enriched GO categories, at the 0.05 level.
— Click on the Help button again to close this help window.
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The GO tree — Molecular Function
HELP
This is one of three sections showing Gene Ontology enrichment of the
current module: in this case for molecular function.
The graph shows the hierarchy of the GO categories, their enrichment
for the current module is color coded, and the blue number beside the
category is the minus log ten p-value of the enrichment. (Calculated
using the standard hypergeometric test.) The color of the arrows code
«is a» (cyan) and «part of» relationships.
The tree was built the following way. First all GO terms with more
significant enrichment p-value than 0.05 were collected. Then all
paths from these terms to the root node of the GO tree were included
too. If a GO term is included more than once in the tree, then the
green numbers show 1) the id of the node, this makes it easier to find
other appereances of the term, and 2) the number of appearences.
Note that the same GO category might show up on the graph many
times. This is because the GO was «straightened» for this
graph, i.e. if there are more paths from a GO term to the root node of
the tree, all of them are included. The green numbers
Move the mouse cursor over the terms to get their definition. Clicking
on them takes you to the corresponding Gene Ontology web page.
If you cannot see a graph here at all, that means that there were no
significantly enriched GO categories, at the 0.05 level.
— Click on the Help button again to close this help window.
molecular_function
Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
catalytic activity
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
UDP-glycosyltransferase activity
Catalysis of the transfer of a glycosyl group from a UDP-sugar to a small hydrophobic molecule.
glucuronosyltransferase activity
Catalysis of the reaction: UDP-glucuronate + acceptor = UDP + acceptor beta-D-glucuronoside.
transferase activity
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
transferase activity, transferring glycosyl groups
Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
transferase activity, transferring hexosyl groups
Catalysis of the transfer of a hexosyl group from one compound (donor) to another (acceptor).
all
This term is the most general term possible
glucuronosyltransferase activity
Catalysis of the reaction: UDP-glucuronate + acceptor = UDP + acceptor beta-D-glucuronoside.
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GO BP test for over-representation
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List of all enriched GO categories (biological processes), at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module annotated with the given GO term, just by chance.
- Count
is the number of genes in the module annotated with the given GO
term.
- Size is the total number of genes (in our universe)
annotated with the GO term.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
GO category.
Clicking on the GO identifiers takes you to the Gene Ontology web
pages.
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| Id | Pvalue | ExpCount | Count | Size | Term |
| GO:0006805 | 6.631e-03 | 0.08196 | 3
UGT1A1, UGT1A6, UGT1A9 | 13 | xenobiotic metabolic process |
| GO:0009410 | 1.112e-02 | 0.1009 | 3
UGT1A1, UGT1A6, UGT1A9 | 16 | response to xenobiotic stimulus |
| GO:0007169 | 2.304e-02 | 0.9457 | 6
CRYAB, EPHB2, IRS2, PILRB, SPARC, TEK | 150 | transmembrane receptor protein tyrosine kinase signaling pathway |
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GO CC test for over-representation
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List of all enriched GO categories (cellular components), at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module annotated with the given GO term, just by chance.
- Count
is the number of genes in the module annotated with the given GO
term.
- Size is the total number of genes (in our universe)
annotated with the GO term.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
GO category.
Clicking on the GO identifiers takes you to the Gene Ontology web
pages.
— Click on the Help button again to close this help window.
| Id | Pvalue | ExpCount | Count | Size | Term |
| GO:0044420 | 1.846e-02 | 0.4036 | 4
MFAP5, SNCA, SPARC, TIMP2 | 64 | extracellular matrix part |
| GO:0043205 | 2.699e-02 | 0.05045 | 2
MFAP5, SNCA | 8 | fibril |
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GO MF test for over-representation
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List of all enriched GO categories (molecular function), at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module annotated with the given GO term, just by chance.
- Count
is the number of genes in the module annotated with the given GO
term.
- Size is the total number of genes (in our universe)
annotated with the GO term.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
GO category.
Clicking on the GO identifiers takes you to the Gene Ontology web
pages.
— Click on the Help button again to close this help window.
| Id | Pvalue | ExpCount | Count | Size | Term |
| GO:0015020 | 7.510e-03 | 0.0776 | 3
UGT1A1, UGT1A6, UGT1A9 | 12 | glucuronosyltransferase activity |
| GO:0008559 | 1.404e-02 | 0.0194 | 2
ABCB1, ABCB4 | 3 | xenobiotic-transporting ATPase activity |
| GO:0015239 | 1.404e-02 | 0.0194 | 2
ABCB1, ABCB4 | 3 | multidrug transporter activity |
| GO:0042910 | 1.404e-02 | 0.0194 | 2
ABCB1, ABCB4 | 3 | xenobiotic transporter activity |
| GO:0008194 | 4.440e-02 | 0.3945 | 4
HAS2, UGT1A1, UGT1A6, UGT1A9 | 61 | UDP-glycosyltransferase activity |
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KEGG Pathway test for over-representation
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List of all enriched KEGG pathways, at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module annotated with the given KEGG pathway, just by chance.
- Count
is the number of genes in the module annotated with the given KEGG
pathway.
- Size is the total number of genes (in our universe)
annotated with the KEGG pathway.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
KEGG pathway.
Clicking on the KEGG identifiers takes you to the KEGG web site.
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| Id | Pvalue | ExpCount | Count | Size | Term |
| 00040 | 6.793e-03 | 0.08584 | 3
UGT1A1, UGT1A6, UGT1A9 | 13 | Pentose and glucuronate interconversions |
| 00150 | 2.181e-02 | 0.1387 | 3
UGT1A1, UGT1A6, UGT1A9 | 21 | Androgen and estrogen metabolism |
| 00830 | 2.668e-02 | 0.1519 | 3
UGT1A1, UGT1A6, UGT1A9 | 23 | Retinol metabolism |
| 00500 | 2.941e-02 | 0.1585 | 3
UGT1A1, UGT1A6, UGT1A9 | 24 | Starch and sucrose metabolism |
| 00860 | 2.941e-02 | 0.1585 | 3
UGT1A1, UGT1A6, UGT1A9 | 24 | Porphyrin and chlorophyll metabolism |
| 00983 | 4.542e-02 | 0.1915 | 3
UGT1A1, UGT1A6, UGT1A9 | 29 | Drug metabolism - other enzymes |
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miRNA test for over-representation
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List of all enriched miRNA families, at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module regulated by the given miRNA family, just by chance.
- Count
is the number of genes in the module regulated by the given miRNA
family.
- Size is the total number of genes (in our universe)
regulated with the given miRNA family.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
miRNA family.
The miRNA regulation data was taken from the TargetScan database.
(Only the conserved sites were used for the current analysis.)
Clicking on the miRNA names takes you to the TargetScan web site.
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Chromosome test for over-representation
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List of all enriched Chromosomes, at the 0.05
p-value level.
The columns:
- ExpCount is the expected number of genes in the
module on the given chromosome, just by chance.
- Count
is the number of genes in the module on the given chromosome.
- Size is the total number of genes (in our universe)
on the given chromosome.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
chromosome.
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A list of all genes in the current module, in alphabetical order. The
size of the text corresponds to the gene scores.
Note that some gene symbols may show up more than once, if many
probes match the same Entrez gene.
Genes with no Entrez mapping are given separately, with their
Affymetrics probe ID.
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Entrez genes
A2Malpha-2-macroglobulin (217757_at), score: 0.57
ABCB1ATP-binding cassette, sub-family B (MDR/TAP), member 1 (209993_at), score: 1
ABCB4ATP-binding cassette, sub-family B (MDR/TAP), member 4 (207819_s_at), score: 0.64
AIM2absent in melanoma 2 (206513_at), score: 0.62
ATP6V1B2ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B2 (201089_at), score: 0.59
BHMT2betaine-homocysteine methyltransferase 2 (219902_at), score: 0.56
C5orf30chromosome 5 open reading frame 30 (221823_at), score: -0.52
CA3carbonic anhydrase III, muscle specific (204865_at), score: 0.6
CDR2Lcerebellar degeneration-related protein 2-like (213230_at), score: -0.54
CRTAPcartilage associated protein (201380_at), score: -0.57
CRYABcrystallin, alpha B (209283_at), score: -0.49
DDX17DEAD (Asp-Glu-Ala-Asp) box polypeptide 17 (208151_x_at), score: 0.67
DDX3XDEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked (201211_s_at), score: 0.56
DIO2deiodinase, iodothyronine, type II (203699_s_at), score: 0.8
EPHB2EPH receptor B2 (209589_s_at), score: 0.66
FAM169Afamily with sequence similarity 169, member A (213954_at), score: 0.62
FAT1FAT tumor suppressor homolog 1 (Drosophila) (201579_at), score: -0.53
FKBP9FK506 binding protein 9, 63 kDa (212169_at), score: -0.6
GAGE4G antigen 4 (207086_x_at), score: 0.95
GAGE6G antigen 6 (208155_x_at), score: 0.89
GATA3GATA binding protein 3 (209604_s_at), score: 0.76
HAS2hyaluronan synthase 2 (206432_at), score: -0.48
HERC5hect domain and RLD 5 (219863_at), score: 0.67
HGSNATheparan-alpha-glucosaminide N-acetyltransferase (218017_s_at), score: -0.58
HIVEP2human immunodeficiency virus type I enhancer binding protein 2 (212642_s_at), score: -0.47
HSPB7heat shock 27kDa protein family, member 7 (cardiovascular) (218934_s_at), score: -0.54
IRS2insulin receptor substrate 2 (209185_s_at), score: -0.55
KIAA0495KIAA0495 (213340_s_at), score: -0.5
L1CAML1 cell adhesion molecule (204584_at), score: 0.57
LRRC2leucine rich repeat containing 2 (219949_at), score: -0.51
MAN2A1mannosidase, alpha, class 2A, member 1 (205105_at), score: -0.51
MARK1MAP/microtubule affinity-regulating kinase 1 (221047_s_at), score: 0.76
MFAP5microfibrillar associated protein 5 (213764_s_at), score: -0.52
MITFmicrophthalmia-associated transcription factor (207233_s_at), score: 0.56
MYO1Cmyosin IC (214656_x_at), score: -0.61
NCRNA00084non-protein coding RNA 84 (214657_s_at), score: 0.58
NEFLneurofilament, light polypeptide (221805_at), score: 0.71
NMUneuromedin U (206023_at), score: 0.56
NONOnon-POU domain containing, octamer-binding (208698_s_at), score: 0.57
NRGNneurogranin (protein kinase C substrate, RC3) (204081_at), score: 0.63
OASL2'-5'-oligoadenylate synthetase-like (210797_s_at), score: 0.96
PDE10Aphosphodiesterase 10A (205501_at), score: 0.58
PILRBpaired immunoglobin-like type 2 receptor beta (220954_s_at), score: 0.6
PTGER3prostaglandin E receptor 3 (subtype EP3) (213933_at), score: -0.51
QPCTglutaminyl-peptide cyclotransferase (205174_s_at), score: -0.49
RABGAP1LRAB GTPase activating protein 1-like (213982_s_at), score: -0.53
RP6-213H19.1serine/threonine protein kinase MST4 (218499_at), score: 0.56
SLC4A4solute carrier family 4, sodium bicarbonate cotransporter, member 4 (203908_at), score: -0.47
SMEK1SMEK homolog 1, suppressor of mek1 (Dictyostelium) (220368_s_at), score: 0.58
SNCAsynuclein, alpha (non A4 component of amyloid precursor) (204466_s_at), score: 0.7
SPARCsecreted protein, acidic, cysteine-rich (osteonectin) (212667_at), score: -0.48
TCEAL2transcription elongation factor A (SII)-like 2 (211276_at), score: 0.78
TEKTEK tyrosine kinase, endothelial (206702_at), score: -0.5
TIMP2TIMP metallopeptidase inhibitor 2 (203167_at), score: -0.5
TMEM47transmembrane protein 47 (209656_s_at), score: -0.51
TMOD1tropomodulin 1 (203661_s_at), score: 0.61
UBL3ubiquitin-like 3 (201535_at), score: -0.55
UGT1A1UDP glucuronosyltransferase 1 family, polypeptide A1 (207126_x_at), score: 0.88
UGT1A6UDP glucuronosyltransferase 1 family, polypeptide A6 (206094_x_at), score: 0.89
UGT1A9UDP glucuronosyltransferase 1 family, polypeptide A9 (204532_x_at), score: 0.87
WT1Wilms tumor 1 (206067_s_at), score: 0.64
Non-Entrez genes
Unknown, score:
HELP
Conditions in the module, given in the same order as on the expression
plot above. Red color means over-expression, green under-expression in
the given condition.
The barplot below shows the condition (sample) scores. A separate bar
is shown for each sample, its height is the corresponding score of the
sample in the module. The red and green numbers on the bars are the
sample scores expressed in percents, i.e. 100% is 1.0.
The red and green lines show the module thresholds, samples above
the red line and below the green line are included in the module.
The different experiments that were part of the study, are separated
by dashed vertical lines.
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| Id | sample | Experiment | ExpName | Array | Syndrome | Cell.line |
| E-GEOD-3407-raw-cel-1437949854.cel | 7 | 4 | Cockayne | hgu133a | CS | eGFP |
| E-GEOD-3407-raw-cel-1437949579.cel | 2 | 4 | Cockayne | hgu133a | none | CSB |
| E-GEOD-3407-raw-cel-1437949938.cel | 8 | 4 | Cockayne | hgu133a | none | CSB |
| E-GEOD-3407-raw-cel-1437949750.cel | 6 | 4 | Cockayne | hgu133a | CS | CSB |
| E-GEOD-3407-raw-cel-1437949721.cel | 5 | 4 | Cockayne | hgu133a | CS | CSB |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland
