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Module #850, TG: 2.4, TC: 2, 116 probes, 116 Entrez genes, 4 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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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.
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extracellular region
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
cellular_component
The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
all
This term is the most general term possible
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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.
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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:0007155 | 3.059e-02 | 5.063 | 14
ADAM23, BCAM, CLDN1, COL15A1, GP1BB, HAPLN1, JUP, LAMA5, MTSS1, NINJ1, PCDH7, PKP2, SCARB1, VCAM1 | 368 | cell adhesion |
| GO:0022610 | 3.059e-02 | 5.063 | 14
ADAM23, BCAM, CLDN1, COL15A1, GP1BB, HAPLN1, JUP, LAMA5, MTSS1, NINJ1, PCDH7, PKP2, SCARB1, VCAM1 | 368 | biological adhesion |
| GO:0048856 | 3.509e-02 | 16.61 | 30
ADAM23, AFP, AGRN, COL15A1, ERAP1, FGFR3, FHL3, FOS, FOXF1, GNG4, GPC4, HHEX, HOXB9, HOXC6, KRAS, LRP5, MSR1, MTSS1, NINJ1, PAPPA2, PDLIM3, PIP5K1C, PLXNB1, SCG2, SLC9A1, SMARCD3, SMO, TGM2, TPD52, VCAM1 | 1207 | anatomical structure development |
| GO:0048518 | 4.874e-02 | 11.67 | 23
AGRN, CASP1, CC2D1A, CFI, ERAP1, FOS, FOXF1, HHEX, KRAS, LITAF, LRP5, MSR1, PCBD1, PLAGL2, PLXNB1, RBM14, SCG2, SLC9A1, SMARCD3, SMO, TGM2, TNFSF4, VCAM1 | 848 | positive regulation of biological process |
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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.
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| Id | Pvalue | ExpCount | Count | Size | Term |
| GO:0005576 | 1.013e-04 | 8.957 | 25
ADAM23, ADAMTS12, AFP, AGRN, APOL1, CA11, CFI, COL15A1, ELSPBP1, ERAP1, GPC4, HAPLN1, IL23A, LAMA5, LILRA5, MMRN2, OLFML2A, PAPPA2, PLTP, PLXNB1, PSG1, PTGDS, SCG2, TNFSF4, VCAM1 | 673 | extracellular region |
| GO:0044421 | 1.309e-02 | 5.004 | 14
ADAMTS12, AFP, AGRN, APOL1, COL15A1, GPC4, HAPLN1, IL23A, LAMA5, MMRN2, OLFML2A, SCG2, TNFSF4, VCAM1 | 376 | extracellular region part |
| GO:0030057 | 2.745e-02 | 0.05324 | 2
JUP, PKP2 | 4 | desmosome |
| GO:0031012 | 3.536e-02 | 2.169 | 8
ADAMTS12, AGRN, COL15A1, GPC4, HAPLN1, LAMA5, MMRN2, OLFML2A | 163 | extracellular matrix |
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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.
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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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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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HELP
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
ADAM23ADAM metallopeptidase domain 23 (206046_at), score: -0.68
ADAMTS12ADAM metallopeptidase with thrombospondin type 1 motif, 12 (221421_s_at), score: 0.75
AFPalpha-fetoprotein (204694_at), score: 0.65
AGRNagrin (212285_s_at), score: -0.64
AK3L1adenylate kinase 3-like 1 (204348_s_at), score: 0.7
ALDOBaldolase B, fructose-bisphosphate (214423_x_at), score: 0.64
ALG3asparagine-linked glycosylation 3, alpha-1,3- mannosyltransferase homolog (S. cerevisiae) (207396_s_at), score: -0.52
APOL1apolipoprotein L, 1 (209546_s_at), score: -0.72
ARID5AAT rich interactive domain 5A (MRF1-like) (213138_at), score: -0.56
BAT2LHLA-B associated transcript 2-like (212068_s_at), score: -0.53
BCAMbasal cell adhesion molecule (Lutheran blood group) (40093_at), score: -0.74
C19orf28chromosome 19 open reading frame 28 (220178_at), score: -0.53
CA11carbonic anhydrase XI (209726_at), score: -0.85
CASP1caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase) (211368_s_at), score: -0.55
CC2D1Acoiled-coil and C2 domain containing 1A (58994_at), score: -0.58
CFIcomplement factor I (203854_at), score: -0.7
CLDN1claudin 1 (218182_s_at), score: -0.58
COL15A1collagen, type XV, alpha 1 (203477_at), score: -0.57
DNAJB5DnaJ (Hsp40) homolog, subfamily B, member 5 (212817_at), score: -0.53
DYNLT3dynein, light chain, Tctex-type 3 (203303_at), score: 0.68
ELOVL2elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2 (213712_at), score: -0.77
ELSPBP1epididymal sperm binding protein 1 (220366_at), score: 0.64
ENPP4ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative function) (204160_s_at), score: 0.71
ERAP1endoplasmic reticulum aminopeptidase 1 (214012_at), score: -0.85
ERN1endoplasmic reticulum to nucleus signaling 1 (207061_at), score: 0.65
FAM102Afamily with sequence similarity 102, member A (212400_at), score: -0.62
FGFR3fibroblast growth factor receptor 3 (204379_s_at), score: -0.54
FHL3four and a half LIM domains 3 (218818_at), score: -0.53
FHOD1formin homology 2 domain containing 1 (218530_at), score: -0.53
FOSv-fos FBJ murine osteosarcoma viral oncogene homolog (209189_at), score: -1
FOXF1forkhead box F1 (205935_at), score: -0.62
GALNT3UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3) (203397_s_at), score: -0.58
GCH1GTP cyclohydrolase 1 (204224_s_at), score: -0.53
GNG4guanine nucleotide binding protein (G protein), gamma 4 (205184_at), score: 0.68
GP1BBglycoprotein Ib (platelet), beta polypeptide (206655_s_at), score: -0.62
GPC4glypican 4 (204983_s_at), score: -0.75
GPR37G protein-coupled receptor 37 (endothelin receptor type B-like) (209631_s_at), score: -0.57
HAPLN1hyaluronan and proteoglycan link protein 1 (205523_at), score: 0.67
HHEXhematopoietically expressed homeobox (215933_s_at), score: -0.87
HOXB9homeobox B9 (216417_x_at), score: 0.77
HOXC6homeobox C6 (206858_s_at), score: 0.71
HSF1heat shock transcription factor 1 (202344_at), score: -0.63
IL23Ainterleukin 23, alpha subunit p19 (211796_s_at), score: -0.73
ISYNA1inositol-3-phosphate synthase 1 (222240_s_at), score: -0.63
JUPjunction plakoglobin (201015_s_at), score: -0.64
KCNK1potassium channel, subfamily K, member 1 (204679_at), score: -0.53
KIAA0556KIAA0556 (213185_at), score: -0.57
KRASv-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (214352_s_at), score: 0.65
KTELC1KTEL (Lys-Tyr-Glu-Leu) containing 1 (218587_s_at), score: -0.58
LAMA5laminin, alpha 5 (210150_s_at), score: -0.64
LILRA5leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 5 (215838_at), score: 0.69
LITAFlipopolysaccharide-induced TNF factor (200706_s_at), score: -0.58
LRP5low density lipoprotein receptor-related protein 5 (209468_at), score: -0.6
MAP3K11mitogen-activated protein kinase kinase kinase 11 (203652_at), score: -0.56
ME3malic enzyme 3, NADP(+)-dependent, mitochondrial (204663_at), score: -0.66
MMRN2multimerin 2 (219091_s_at), score: 0.66
MSR1macrophage scavenger receptor 1 (208423_s_at), score: 0.77
MTSS1metastasis suppressor 1 (203037_s_at), score: -0.6
NINJ1ninjurin 1 (203045_at), score: -0.72
NXPH4neurexophilin 4 (221967_at), score: -0.57
OLFML2Aolfactomedin-like 2A (213075_at), score: -0.54
PAPPA2pappalysin 2 (213332_at), score: -0.78
PCBD1pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (203557_s_at), score: -0.59
PCDH7protocadherin 7 (205534_at), score: -0.52
PDE1Cphosphodiesterase 1C, calmodulin-dependent 70kDa (207303_at), score: 0.93
PDE4Aphosphodiesterase 4A, cAMP-specific (phosphodiesterase E2 dunce homolog, Drosophila) (204735_at), score: -0.55
PDK2pyruvate dehydrogenase kinase, isozyme 2 (202590_s_at), score: -0.52
PDLIM3PDZ and LIM domain 3 (209621_s_at), score: -0.76
PHKA2phosphorylase kinase, alpha 2 (liver) (209439_s_at), score: -0.55
PIP5K1Cphosphatidylinositol-4-phosphate 5-kinase, type I, gamma (212518_at), score: -0.61
PKP2plakophilin 2 (207717_s_at), score: -0.87
PLAGL2pleiomorphic adenoma gene-like 2 (202925_s_at), score: -0.65
PLTPphospholipid transfer protein (202075_s_at), score: -0.58
PLXNB1plexin B1 (215807_s_at), score: -0.55
PNMAL1PNMA-like 1 (218824_at), score: -0.58
PSG1pregnancy specific beta-1-glycoprotein 1 (208257_x_at), score: 0.66
PSG3pregnancy specific beta-1-glycoprotein 3 (215821_x_at), score: 0.76
PTGDSprostaglandin D2 synthase 21kDa (brain) (212187_x_at), score: -0.83
PTPREprotein tyrosine phosphatase, receptor type, E (221840_at), score: -0.55
RAB33ARAB33A, member RAS oncogene family (206039_at), score: -0.53
RAMP1receptor (G protein-coupled) activity modifying protein 1 (204916_at), score: -0.59
RARRES3retinoic acid receptor responder (tazarotene induced) 3 (204070_at), score: -0.74
RBM14RNA binding motif protein 14 (204178_s_at), score: -0.53
RHBDF2rhomboid 5 homolog 2 (Drosophila) (219202_at), score: -0.53
RRP1ribosomal RNA processing 1 homolog (S. cerevisiae) (218758_s_at), score: -0.55
SCARB1scavenger receptor class B, member 1 (201819_at), score: -0.87
SCG2secretogranin II (chromogranin C) (204035_at), score: -0.94
SENP5SUMO1/sentrin specific peptidase 5 (213184_at), score: -0.67
SGPL1sphingosine-1-phosphate lyase 1 (212322_at), score: -0.55
SIN3BSIN3 homolog B, transcription regulator (yeast) (209352_s_at), score: -0.56
SLC12A7solute carrier family 12 (potassium/chloride transporters), member 7 (218066_at), score: -0.59
SLC24A6solute carrier family 24 (sodium/potassium/calcium exchanger), member 6 (218749_s_at), score: -0.54
SLC9A1solute carrier family 9 (sodium/hydrogen exchanger), member 1 (209453_at), score: -0.64
SMARCD3SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 (204099_at), score: -0.57
SMG1SMG1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans) (210057_at), score: 0.64
SMOsmoothened homolog (Drosophila) (218629_at), score: -0.56
SSBP3single stranded DNA binding protein 3 (217991_x_at), score: -0.66
STAP2signal transducing adaptor family member 2 (221610_s_at), score: 0.63
STAT2signal transducer and activator of transcription 2, 113kDa (205170_at), score: 0.68
TGM2transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase) (201042_at), score: -0.55
TM6SF1transmembrane 6 superfamily member 1 (219892_at), score: -0.76
TM7SF2transmembrane 7 superfamily member 2 (210130_s_at), score: -0.54
TMCO6transmembrane and coiled-coil domains 6 (221096_s_at), score: 0.68
TMEM132Atransmembrane protein 132A (218834_s_at), score: -0.75
TMEM222transmembrane protein 222 (221512_at), score: -0.53
TNFSF4tumor necrosis factor (ligand) superfamily, member 4 (207426_s_at), score: -0.67
TNIKTRAF2 and NCK interacting kinase (213107_at), score: -0.64
TOM1target of myb1 (chicken) (202807_s_at), score: -0.53
TPCN1two pore segment channel 1 (217914_at), score: -0.55
TPD52tumor protein D52 (201690_s_at), score: -0.67
TRIB2tribbles homolog 2 (Drosophila) (202478_at), score: -0.57
VCAM1vascular cell adhesion molecule 1 (203868_s_at), score: -0.6
WDR91WD repeat domain 91 (218971_s_at), score: 0.65
WT1Wilms tumor 1 (206067_s_at), score: -0.56
ZNF35zinc finger protein 35 (206096_at), score: -0.68
ZNF711zinc finger protein 711 (207781_s_at), score: -0.78
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 |
| 46A.CEL | 1 | 3 | DS-mosaic | hgu133plus2 | none | DS-mosaic 1 |
| 46B.CEL | 2 | 3 | DS-mosaic | hgu133plus2 | none | DS-mosaic 2 |
| E-GEOD-3407-raw-cel-1437949557.cel | 1 | 4 | Cockayne | hgu133a | CS | eGFP |
| 47C.CEL | 5 | 3 | DS-mosaic | hgu133plus2 | Down mosaic | DS-mosaic 5 |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland
