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Supplamentary Data Table S3: MARQ analysis for common gene expression signatures of Hodgkin's lymphoma
Datasets were extracted from Steidl et al., 2008 (ref. 7) and are available at the GEO database: http://www.ncbi.nlm.nih.gov/geo/ (GEO accession numbers: GSE39132,GSE39134)
Details on MARQ analysis score and p-value are available at: http://marq.dacya.ucm.es/ (ref. 28)
Only gene signatures with p-value < 0.0001 are presented.
MARQ analysis for genes differentially regulated in HRS cells from patients with good cHL outcome vs. bad cHL outcome (GEO accession number: GSE39132)
Common gene signatures
Score
P-Val
[+]Squamous cell lung carcinomas [GEO] stage Ia <=> stage IIIa (disease.state)
0,788
< 0.0001
[+]Cytosine arabinoside effect on Ewing’s sarcoma cell line: time course and dose response [GEO] cytosine arabinoside <=> DMSO (agent)
0,754
< 0.0001
[+]Myeloid leukemia cell lines [GEO] monocyte <=> U937 [ratio] (cell.line)
0,749
< 0.0001
[+]Malignant pleural mesothelioma [GEO] pleural <=> mesothelial cell line (cell.type)
0,733
< 0.0001
[+]Endoplasmic reticulum membrane-associated genes in breast cancer cell line MCF-7 [GEO] membrane fraction <=> cytosolic fraction (protocol)
0,72
< 0.0001
[+]Early onset colorectal cancer: normal-appearing colonic mucosa [GEO] early onset colorectal cancer <=> healthy control (disease.state)
0,717
< 0.0001
[+]Serrated and conventional adenocarcinomas [GEO] serrated colerectal carcinoma <=> conventional colorectal carcinoma (disease.state)
0,714
< 0.0001
[+]Malignant fibrous histiocytoma and various soft tissue sarcomas [GEO] well-differentiated liposarcoma <=> synovial sarcoma (disease.state)
0,705
< 0.0001
[+]Oncogene Signature Dataset [GEO] Src <=> Myc (knockdown)
0,693
< 0.0001
[+]Ductal carcinoma in situ to invasive ductal carcinoma progression (HG-U133 2.0) [GEO] IDC <=> DCIS (disease.state)
0,674
< 0.0001
[+]Tamoxifen effect on breast cancer cell line expressing estrogen receptor alpha and beta [GEO] adenovirus carrying estrogen receptor beta <=> control adenovirus (infection)
0,666
< 0.0001
[+]IFN-gamma and IL-1beta effect on thyroid epithelial cells (HG-U133A 2.0) [GEO] IFN-gamma <=> control (agent)
0,664
< 0.0001
[+]Estrogen positive breast cancer recurrence during tamoxifen therapy: whole tissue tumor [GEO] cancer recurred (disease.state)
0,654
< 0.0001
[+]Breast cancer cell expression profiles (HG-U133A) [GEO] mammary epithelium <=> HCC 1954 (cell.line)
0,654
< 0.0001
[+]Glial brain tumors [GEO] glioblastoma (disease.state)
0,652
< 0.0001
[+]Primary effusion lymphomas and associated viral infections [GEO] mononuclear cell <=> cell line (cell.type)
0,645
< 0.0001
[+]Estrogen positive breast cancer recurrence during tamoxifen therapy: whole tissue tumor [GEO] disease-free (disease.state)
0,645
< 0.0001
[+]Renal clear cell carcinoma (HG-U133A) [GEO] RCC <=> normal (disease.state)
0,63
< 0.0001
[+]Leukotriene LTD4 effect on macrophage and endothelial cells [GEO] umbilical vein endothelial <=> macrophage (cell.type)
0,628
< 0.0001
[+]Aplidin and cytarabine effect on diffuse large B cell lymphoma cell line [GEO] in vivo <=> in vitro (protocol)
0,623
< 0.0001
[+]Ionizing radiation effect on monocytic leukemia cells [GEO] irradiated <=> untreated (other)
0,614
< 0.0001
[+]Myelodysplastic syndromes: CD34+ cells [GEO] refractory anemia <=> normal (disease.state)
0,602
< 0.0001
[+]miR-124 overexpression: time course [GEO] 72 h <=> 32 h (time)
0,601
< 0.0001
[+]Measles: peripheral blood mononuclear cells [GEO] discharge <=> control (protocol)
0,595
< 0.0001
[+]Melanoma progression [GEO] melanoma in situ <=> normal (disease.state)
0,593
< 0.0001
[+]Multiple myeloma molecular classification [GEO] TC4 <=> TC2 (cell.type)
0,593
< 0.0001
[+]Prostate cancer progression [GEO] primary <=> metastatic (disease.state)
0,592
< 0.0001
MARQ analysis for genes differentially regulated in 5 Hodgkin lymphoma cell lines profiles vs. 5 CD77+ cell profiles (GEO accession number: GSE39134)
Common gene signatures
Score
P-Val
[+]Primary effusion lymphomas and associated viral infections [GEO] KSHV-positive EBV-negative <=> KSHV-negative EBV-positive (infection)
0,991
< 0.0001
[+]Primary effusion lymphomas and associated viral infections [GEO] KSHV-positive EBV-positive <=> KSHV-negative EBV-positive (infection)
0,956
< 0.0001
[+]Myelodysplastic syndromes: CD34+ cells [GEO] refractory anemia with ringed sideroblasts <=> normal (disease.state)
0,898
< 0.0001
[+]Myelodysplastic syndromes: CD34+ cells [GEO] refractory anemia with excess blasts <=> normal (disease.state)
0,846
< 0.0001
[+]Metastatic melanoma: peripheral blood lymphocytes [GEO] CD8 T cell (cell.type)
0,835
< 0.0001
[+]Waldenstrom's macroglobulinemia: B lymphocytes and plasma cells [GEO] multiple myeloma <=> normal (disease.state)
0,814
< 0.0001
[+]B-cell chronic lymphocytic leukemia cell type and prognosis [GEO] poor prognosis <=> good prognosis (other)
0,781
< 0.0001
[+]Endometrium throughout the menstrual cycle [GEO] proliferative phase <=> ambiguous phase (other)
0,765
< 0.0001
[+]Nicotinamide effect on thrombopoietin-induced megakaryocyte differentiation in vitro [GEO] 1 d (time)
0,762
< 0.0001
[+]Metastatic melanoma: peripheral blood lymphocytes [GEO] CD4 T cell (cell.type)
0,744
< 0.0001
[+]Myelodysplastic syndromes: CD34+ cells [GEO] refractory anemia <=> normal (disease.state)
0,742
< 0.0001
[+]CD4+ T cell differentiation (HG-133B) [GEO] stromal <=> CD4 (cell.type)
0,738
< 0.0001
[+]High-grade gliomas (HG-U133A) [GEO] unknown <=> more than 209 wk survival (other)
0,731
< 0.0001
[+]Non-diseased lung tissue [GEO] non-smoker <=> former smoker (stress)
0,731
< 0.0001
[+]Metastatic melanoma: peripheral blood lymphocytes [GEO] Natural killer (NK) cell (cell.type)
0,73
< 0.0001
[+]Multiple myeloma molecular classification [GEO] TC4 <=> TC1 (cell.type)
0,727
< 0.0001
[+]miR-124 overexpression: time course [GEO] 24 h <=> 4 h (time)
0,724
< 0.0001
[+]Melanoma progression [GEO] epidermal keratinocyte culture <=> biopsy (specimen)
0,723
< 0.0001
[+]Measles: peripheral blood mononuclear cells [GEO] discharge <=> control (protocol)
0,713
< 0.0001
[+]Multiple myeloma molecular classification [GEO] TC3 <=> TC1 (cell.type)
0,706
< 0.0001
[+]Mast cell activation via the Fc(epsilon)RI [GEO] batch S8 (other)
0,705
< 0.0001
[+]Papillary renal cell carcinoma classification [GEO] histologic class 1 and 2A <=> histologic class 1 (disease.state)
0,698
< 0.0001
[+]Idiopathic myelofibrosis: hematopoietic CD34+ stem cells [GEO] idiopathic myelofibrosis <=> normal (disease.state)
0,695
< 0.0001
[+]Anti-cancer agent sapphyrin PCI-2050 effect on lung cancer cell line: dose response [GEO] 5 ug/ml <=> 5% (dose)
0,694
< 0.0001
[+]Myelodysplastic syndrome [GEO] myelodysplastic syndrome <=> normal (disease.state)
0,693
< 0.0001
[+]Glioma-derived stem cell factor effect on angiogenesis in the brain [GEO] tumor grade IV <=> tumor grade II (tissue)
0,691
< 0.0001
[+]Epstein-Barr virus nuclear antigen 2 activation [GEO] EBNA-2 activated <=> control (protocol)
0,69
< 0.0001
[+]Melanoma progression [GEO] metastatic melanoma cell culture <=> biopsy (specimen)
0,681
< 0.0001
[+]Monocyte differentiation to macrophage and subsequent polarization (HG-U133A) [GEO] monocyte at intermediate differentiation stage <=> monocyte (development.stage)
0,681
< 0.0001
[+]Papillary thyroid cancer [GEO] papillary thyroid cancer <=> normal (disease.state)
0,676
< 0.0001
[+]Hematopoietic stem cell engraftment in goat [GEO] liver <=> blood (tissue)
0,675
< 0.0001
[+]Aplidin and cytarabine effect on diffuse large B cell lymphoma cell line [GEO] in vivo <=> in vitro (protocol)
0,666
< 0.0001
[+]Endometriosis [GEO] proliferative <=> early secretory (other)
0,666
< 0.0001
[+]Papillary renal cell carcinoma classification [GEO] histologic class 2A <=> histologic class 1 (disease.state)
0,665
< 0.0001
[+]Myelodysplastic syndrome [GEO] rheumatoid arthritis, on methotrexate <=> normal (disease.state)
0,663
< 0.0001
[+]Malignant pleural mesothelioma [GEO] mesothelial cell line <=> lung (cell.type)
0,655
< 0.0001