Background
Methods
Integration and cross-validation of microarrays data
Study | First sample (day of cycle, number of samples) | Second sample (day of cycle, number of samples) | Microarrays platform | Fold-change cut-off value | N° of up-regulated transcripts | N° of down-regulated transcripts |
---|---|---|---|---|---|---|
Kao et al. (2002) [11] | Proliferative phase (8-11, n = 4) | Mid-secretory (21-23, n = 7) | Affymetrix Hu95A | ≥2.0 | 156 | 377 |
Carson et al. (2002) [13] | Early-secretory (15-17, n = 3*) | Mid-secretory (20-22, n = 3*) | Affymetrix Hu95A | ≥2.0 | 323 | 370 |
Borthwick et al. (2003) [12] | Proliferative phase (9-11, n = 5*) | Mid-secretory (19-21, n = 5*) | Affymetrix Hu95A-E | ≥2.0 | 90 | 46 |
Riesewijk et al. (2003) [14] | Early-secretory (15, n = 5) | Mid-secretory (20, n = 5) | Affymetrix Hu95A | ≥3.0 | 153 | 58 |
Mirkin et al. (2005) [15] | Early-secretory (16, n = 3) | Mid-secretory (21, n = 5) | Affymetrix HG_U95Av2 | ≥2.0 | 49 | 58 |
Talbi et al. (2006)¶ [9] | Early-secretory (n = 3) | Mid-secretory (n = 8) | Affymetrix HG-U133 plus 2.0 | ≥1.5 | 1415 | 1463 |
Haouzi et al. (2009)† [18] | Early-secretory (16, n = 31) | Mid-secretory (20, n = 31) | Affymetrix HG-U133 plus 2.0 | ≥2.0 | 945 | 67 |
Functional clustering
TFBS detection in promoter regions of genes associated to endometrial receptivity
Results
Identification of genes associated to endometrial receptivity
UniGene ID | Gene Symbol | Gene Title | Kao et al.(2002) [11] | Carson et al.(2002) [13] | Borthwick et al.(2003) [12] | Riesewijk et al.(2003) [14] | Mirkin et al.(2005) [15] | Talbi et al.(2006) [9] | Haouzi et al.(2009) [18] |
---|---|---|---|---|---|---|---|---|---|
Hs.1012 | C4BPA | complement component 4 binding protein, alpha | ↑ | ↑ | ↑ | ↑ | ↑ | ↑ | |
Hs.313 | SPP1 | secreted phosphoprotein 1 (osteopontin, bone sialoprotein I, early T-lymphocyte activation 1) | ↑ | ↑ | ↑ | ↑ | ↑ | ↑ | |
Hs.522555 | APOD | apolipoprotein D | ↑ | ↑ | ↑ | ↑ | ↑ | ||
Hs.126517 | CD55 | Decay accelerating factor for complement | ↑ | ↑ | ↑ | ↑ | ↑ | ||
Hs.155597 | CFD | complement factor D (adipsin) | ↑ | ↑ | ↑ | ↑ | ↑ | ||
Hs.647036 | CLDN4 | claudin 4 | ↑ | ↑ | ↑ | ↑ | ↑ | ||
Hs.40499 | DKK1 | dickkopf homolog 1 (Xenopus laevis) | ↑ | ↑ | ↑ | ↑ | ↑ | ||
Hs.519601 | ID4 | Inhibitor of DNA binding 4, dominant negative helix-loop-helix protein | ↑ | ↑ | ↑ | ↑ | ↑ | ||
Hs.654378 | IL15 | interleukin 15 | ↑ | ↑ | ↑ | ↑ | ↑ | ||
Hs.186486 | MAP3K5 | mitogen-activated protein kinase kinase kinase 5 | ↑ | ↑ | ↑ | ↑ | ↑ | ||
Hs.511605 | ANXA2 | annexin A2 | ↑ | ↑ | ↑ | ↑ | |||
Hs.422986 | ANXA4 | annexin A4 | ↑ | ↑ | ↑ | ↑ | |||
Hs.524224 | C1R | complement component 1, r subcomponent | ↑ | ↑ | ↑ | ↑ | |||
Hs.80409 | GADD45A | growth arrest and DNA-damage-inducible, alpha | ↑ | ↑ | ↑ | ↑ | |||
Hs.386567 | GBP2 | guanylate binding protein 2, interferon-inducible | ↑ | ↑ | ↑ | ↑ | |||
Hs.183109 | MAOA | monoamine oxidase A | ↑ | ↑ | ↑ | ↑ | |||
Hs.532325 | PAEP | progestagen-associated endometrial protein (glycodelin) | ↑ | ↑ | ↑ | ↑ | |||
Hs.384598 | SERPING1 | serpin peptidase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary) | ↑ | ↑ | ↑ | ↑ | |||
Hs.1584 | COMP | cartilage oligomeric matrix protein | ↑ | ↑ | ↑ | ||||
Hs.558314 | CP | ceruloplasmin (ferroxidase) | ↑ | ↑ | ↑ | ||||
Hs.368912 | DPP4 | dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein 2) | ↑ | ↑ | ↑ | ||||
Hs.446392 | DYNLT3 | Dynein, light chain, Tctex-type 3 | ↑ | ↑ | ↑ | ||||
Hs.198862 | FBLN2 | fibulin 2 | ↑ | ↑ | ↑ | ||||
Hs.433300 | FCER1G | Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide | ↑ | ↑ | ↑ | ||||
Hs.432132 | G0S2 | G0/G1switch 2 | ↑ | ↑ | ↑ | ||||
Hs.2681 | GAST | gastrin | ↑ | ↑ | ↑ | ||||
Hs.616962 | GDF15 | growth differentiation factor 15 | ↑ | ↑ | ↑ | ||||
Hs.105806 | GNLY | granulysin | ↑ | ↑ | ↑ | ||||
Hs.386793 | GPX3 | glutathione peroxidase 3 (plasma) | ↑ | ↑ | ↑ | ||||
Hs.497636 | LAMB3 | laminin, beta 3 | ↑ | ↑ | ↑ | ||||
Hs.433391 | MT1G | Metallothionein-IG | ↑ | ↑ | ↑ | ||||
Hs.262857 | PRUNE2 | Prune homolog 2 (Drosophila) | ↑ | ↑ | ↑ | ||||
Hs.50223 | RBP4 | retinol binding protein 4, plasma | ↑ | ↑ | ↑ | ||||
Hs.654444 | S100A4 | S100 calcium binding protein A4 | ↑ | ↑ | ↑ | ||||
Hs.2962 | S100P | S100 calcium binding protein P | ↑ | ↑ | ↑ | ||||
Hs.517070 | SLPI | secretory leukocyte peptidase inhibitor | ↑ | ↑ | ↑ | ||||
Hs.517033 | TGM2 | transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase) | ↑ | ↑ | ↑ | ||||
Hs.525607 | TNFAIP2 | tumor necrosis factor, alpha-induced protein 2 | ↑ | ↑ | ↑ | ||||
Hs.695930 | VCAN | versican | ↑ | ↑ | ↑ | ||||
Hs.2157 | WAS | Wiskott-Aldrich syndrome (eczema-thrombocytopenia) | ↑ | ↑ | ↑ |
UniGene ID | Gene Symbol | Gene Title | Kao et al.(2002) [11] | Carson et al.(2002) [13] | Borthwick et al.(2003) [12] | Riesewijk et al.(2003) [14] | Mirkin et al.(2005) [15] | Talbi et al.(2006) [9] |
---|---|---|---|---|---|---|---|---|
Hs.522484 | OLFM1 | olfactomedin 1 | ↓ | ↓ | ↓ | ↓ | ↓ | |
Hs.23960 | CCNB1 | cyclin B1 | ↓ | ↓ | ↓ | ↓ | ||
Hs.405662 | CRABP2 | cellular retinoic acid binding protein 2 | ↓ | ↓ | ↓ | ↓ | ||
Hs.1408 | EDN3 | endothelin 3 | ↓ | ↓ | ↓ | ↓ | ||
Hs.264887 | FGFR1 | fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2, Pfeiffer syndrome) | ↓ | ↓ | ↓ | ↓ | ||
Hs.424414 | MSX1 | msh homeobox 1 | ↓ | ↓ | ↓ | ↓ | ||
Hs.89404 | MSX2 | msh homeobox 2 | ↓ | ↓ | ↓ | ↓ | ||
Hs.523852 | CCND1 | cyclin D1 | ↓ | ↓ | ↓ | |||
Hs.524947 | CDC20 | cell division cycle 20 homolog (S. cerevisiae) | ↓ | ↓ | ↓ | |||
Hs.1594 | CENPA | centromere protein A | ↓ | ↓ | ↓ | |||
Hs.83758 | CKS2 | CDC28 protein kinase regulatory subunit 2 | ↓ | ↓ | ↓ | |||
Hs.530904 | CSRP2 | cysteine and glycine-rich protein 2 | ↓ | ↓ | ↓ | |||
Hs.367725 | GATA2 | GATA binding protein 2 | ↓ | ↓ | ↓ | |||
Hs.596913 | HPGD | hydroxyprostaglandin dehydrogenase 15-(NAD) | ↓ | ↓ | ↓ | |||
Hs.654504 | IHH | Indian hedgehog homolog (Drosophila) | ↓ | ↓ | ↓ | |||
Hs.438720 | MCM7 | Minichromosome maintenance complex component 7 | ↓ | ↓ | ↓ | |||
Hs.75823 | MLLT11 | Myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 11 | ↓ | ↓ | ↓ | |||
Hs.143751 | MMP11 | matrix metallopeptidase 11 (stromelysin 3) | ↓ | ↓ | ↓ | |||
Hs.2256 | MMP7 | Matrix metalloproteinase 7 | ↓ | ↓ | ↓ | |||
Hs.658169 | SFRP4 | secreted frizzled-related protein 4 | ↓ | ↓ | ↓ | |||
Hs.182231 | TRH | thyrotropin-releasing hormone | ↓ | ↓ | ↓ |
Functional associations of transcripts from CERTL
Database | Functional annotation | number of genes | p Value |
---|---|---|---|
up-regulated transcripts
| |||
Gene Ontology | response to stimulus | 16 | <0.0001 |
Gene Ontology | response to biotic stimulus | 12 | <0.0001 |
Gene Ontology
|
defense response
|
11
|
<0.0001
|
Gene Ontology
|
immune response
|
10
|
<0.0001
|
Gene Ontology | response to stress | 9 | 0.0001 |
Gene Ontology
|
complement activation, classical pathway
|
4
|
<0.0001
|
Gene Ontology
|
complement activation
|
4
|
<0.0001
|
KEGG Pathway
|
Complement and coagulation cascades
|
4
|
0.0002
|
down-regulated transcripts
| |||
Gene Ontology | morphogenesis | 10 | 0.0001 |
Gene Ontology
|
cytokinesis
|
4
|
0.0001
|
Gene Ontology | skeletal development | 4 | 0.0001 |
Gene Ontology | development | 12 | 0.0002 |
KEGG Pathway
|
cell cycle
|
4
|
0.0002
|
Database | Functional annotation | number of genes | p Value |
---|---|---|---|
up-regulated transcripts
| |||
GOTERM_CC_FAT | extracellular region | 22 | <0.0001 |
SP_PIR_KEYWORDS | signal | 22 | <0.0001 |
UP_SEQ_FEATURE | signal peptide | 22 | <0.0001 |
GOTERM_BP_FAT
|
defense response
|
9
|
<0.0001
|
GOTERM_BP_FAT
|
positive regulation of immune response
|
7
|
<0.0001
|
GOTERM_BP_FAT
|
inflammatory response
|
7
|
<0.0001
|
GOTERM_BP_FAT
|
immune effector process
|
6
|
<0.0001
|
GOTERM_BP_FAT
|
complement activation
|
5
|
<0.0001
|
GOTERM_BP_FAT
|
immunoglobulin mediated immune response
|
5
|
<0.0001
|
GOTERM_BP_FAT
|
lymphocyte mediated immunity
|
5
|
<0.0001
|
GOTERM_BP_FAT
|
activation of immune response
|
5
|
<0.0001
|
KEGG_PATHWAY
|
Complement and coagulation cascades
|
5
|
<0.0001
|
SP_PIR_KEYWORDS
|
complement pathway
|
4
|
<0.0001
|
GOTERM_BP_FAT | response to steroid hormone stimulus | 4 | 0.0068 |
GOTERM_BP_FAT | cell cycle | 7 | 0.0038 |
down-regulated transcripts
| |||
GOTERM_BP_FAT | response to steroid hormone stimulus | 4 | 0.0068 |
SP_PIR_KEYWORDS
|
cell cycle
|
6
|
0.00045
|
KEGG_PATHWAY
|
cell cycle
|
4
|
0.0038
|
GOTERM_BP_FAT
|
cell division
|
5
|
0.0028
|
GOTERM_BP_FAT
|
cell cycle
|
7
|
0.0038
|
GOTERM_BP_FAT
|
regulation of cell cycle
|
6
|
0.00047
|
SP_PIR_KEYWORDS | developmental protein | 6 | 0.0041 |
UP_SEQ_FEATURE | metal ion-binding site:Zinc 1 | 3 | 0.0053 |
Identification of consensus sequences for TFBS sites of CERTL
Up-regulated genes | Down-regulated genes | ||||||
---|---|---|---|---|---|---|---|
Tool for TFBS analysis | Transcription factor name | TFBS matrix | p Value | Tool for TFBS analysis | Transcription factor name | TFBS matrix | p Value |
MotifScanner |
E47
| TRANSFAC | 0.008 | MotifScanner |
E47
| TRANSFAC | 0.002 |
MEF2
| TRANSFAC | 0.002 |
SREBP1
| TRANSFAC | 0.007 | ||
SREBP1
| TRANSFAC | 0.007 |
ARNT
| TRANSFAC | 0.001 | ||
TELIS | PBX1 | TRANSFAC | 0.0001 | TELIS |
ARNT
| TRANSFAC | <0.0001 |
AP1 | TRANSFAC | 0.0005 | HNF1 | TRANSFAC | 0.007 | ||
EVI1 | TRANSFAC | 0.002 | HNF-1 | JASPAR | 0.007 | ||
SOX5 | TRANSFAC | 0.003 | OTFBS | Hb | TRANSFAC | <0.0001 | |
Sox-5 | JASPAR | 0.0031 | BR-C Z1 | TRANSFAC | <0.0001 | ||
Pbx1 | JASPAR | 0.007 | BR-C Z4 | TRANSFAC | 0.004 | ||
FREAC-2
| JASPAR | 0.007 | HFH-2 | TRANSFAC | <0.0001 | ||
SOX-9 | JASPAR | 0.008 | HFH-3 | TRANSFAC | <0.0001 | ||
OTFBS | GCN4 | TRANSFAC | 0.001 | FOXJ2 | TRANSFAC | <0.0001 | |
CP2 | TRANSFAC | 0.007 | GATHER | NFY | TRANSFAC | 0.004 | |
Ik-2 | TRANSFAC | <0.0001 |
E2F1
| TRANSFAC | 0.006 | ||
Bcd | TRANSFAC | <0.0001 | DEAF1 | TRANSFAC | 0.007 | ||
ARP-1 | TRANSFAC | <0.0001 | |||||
MEF-2
| TRANSFAC | 0.005 | |||||
cap | TRANSFAC | 0.004 | |||||
E47
| TRANSFAC | 0.002 | |||||
SREBP-1
| TRANSFAC | <0.0001 | |||||
GATHER | SRF | TRANSFAC | 0.001 | ||||
NRF2 | TRANSFAC | 0.002 | |||||
E2F1
| TRANSFAC | 0.002 | |||||
FREAC2
| TRANSFAC | 0.003 | |||||
HEB | TRANSFAC | 0.004 | |||||
ELK1 | TRANSFAC | 0.005 |