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pmid:32429566

Metabolic Plasticity in Ovarian Cancer Stem Cells.

Alia Ghoneum · Daniela Gonzalez · Ammar Yasser Abdulfattah · Neveen Said

Cancers · 2020 doi:10.3390/cancers12051267

Paper

complete

Experiment

complete

Data

partial

Analysis

partial

Execution

absent

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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2026-11-01T15:41:02Z
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title
Metabolic Plasticity in Ovarian Cancer Stem Cells.
doi
10.3390/cancers12051267
pmid
32429566
authors array · 4 items
[0]
Alia Ghoneum
[1]
Daniela Gonzalez
[2]
Ammar Yasser Abdulfattah
[3]
Neveen Said
journal
Cancers
year
2020
abstract
Ovarian Cancer is the fifth most common cancer in females and remains the most lethal gynecological malignancy as most patients are diagnosed at late stages of the disease. Despite initial responses to therapy, recurrence of chemo-resistant disease is common. The presence of residual cancer stem cells (CSCs) with the unique ability to adapt to several metabolic and signaling pathways represents a major challenge in developing novel targeted therapies. The objective of this study is to investigate the transcripts of putative ovarian cancer stem cell (OCSC) markers in correlation with transcripts of receptors, transporters, and enzymes of the energy generating metabolic pathways involved in high grade serous ovarian cancer (HGSOC). We conducted correlative analysis in data downloaded from The Cancer Genome Atlas (TCGA), studies of experimental OCSCs and their parental lines from Gene Expression Omnibus (GEO), and Cancer Cell Line Encyclopedia (CCLE). We found positive correlations between the transcripts of OCSC markers, specifically CD44, and glycolytic markers. TCGA datasets revealed that NOTCH1, CD133, CD44, CD24, and ALDH1A1, positively and significantly correlated with tricarboxylic acid cycle (TCA) enzymes. OVCAR3-OCSCs (cancer stem cells derived from a well-established epithelial ovarian cancer cell line) exhibited enrichment of the electron transport chain (ETC) mainly in complexes I, III, IV, and V, further supporting reliance on the oxidative phosphorylation (OXPHOS) phenotype. OVCAR3-OCSCs also exhibited significant increase in CD36, ACACA, SCD, and CPT1A, with CD44, CD133, and ALDH1A1 exhibiting positive correlations with lipid metabolic enzymes. TCGA data show positive correlations between OCSC markers and glutamine metabolism enzymes, whereas in OCSC experimental models of GSE64999, GSE28799, and CCLE, the number of positive and negative correlations observed was significantly lower and was different between model systems. Appropriate integration and validation of data model systems with those in patients' specimens is needed not only to bridge our knowledge gap of metabolic programing of OCSCs, but also in designing novel strategies to target the metabolic plasticity of dormant, resistant, and CSCs.
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The differential expression of the OCSCs markers and the enzymes involved in the metabolic pathways in OCSCs and their parental cells was analyzed by the multiple t-test with Holm–Sidak method, and each gene was analyzed individually between the two groups, without assuming a consistent SD with p ≤ 0.05.
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sections[4] "2.2. Data Analysis" paragraph 2
quote
The differential expression of the OCSCs markers and the enzymes involved in the metabolic pathways in OCSCs and their parental cells was analyzed by the multiple t-test with Holm–Sidak method, and each gene was analyzed individually between the two groups, without assuming a consistent SD with p ≤ 0.05.
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Gene expression profiles of two studies of OCSC GSE28799 [41] and GSE64999 [42] with platform information of GPL570 and GPL17077, respectively, were extracted from Gene Expression Omnibus (GEO). Both included ovarian cancer spheroids and their parental cells. GSE28799 included OVCAR3-derived spheroids and their parental OVCAR3 in triplicates.
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sections[3] "2.1. Microarray Extraction" paragraph 2
quote
Gene expression profiles of two studies of OCSC GSE28799 [41] and GSE64999 [42] with platform information of GPL570 and GPL17077, respectively, were extracted from Gene Expression Omnibus (GEO). Both included ovarian cancer spheroids and their parental cells. GSE28799 included OVCAR3-derived spheroids and their parental OVCAR3 in triplicates.
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Gene expression profiles of two studies of OCSC GSE28799 [41] and GSE64999 [42] with platform information of GPL570 and GPL17077, respectively, were extracted from Gene Expression Omnibus (GEO). Both included ovarian cancer spheroids and their parental cells. GSE28799 included OVCAR3-derived spheroids and their parental OVCAR3 in triplicates.
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Gene expression profiles of two studies of OCSC GSE28799 [41] and GSE64999 [42] with platform information of GPL570 and GPL17077, respectively, were extracted from Gene Expression Omnibus (GEO). Both included ovarian cancer spheroids and their parental cells. GSE28799 included OVCAR3-derived spheroids and their parental OVCAR3 in triplicates.
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Isolation and characterization of stem-like cells from a human ovarian cancer cell line
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Gene expression profiles of two studies of OCSC GSE28799 [41] and GSE64999 [42] with platform information of GPL570 and GPL17077, respectively, were extracted from Gene Expression Omnibus (GEO). Both included ovarian cancer spheroids and their parental cells. GSE28799 included OVCAR3-derived spheroids and their parental OVCAR3 in triplicates.
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Gene regulation during differentiation of ovarian cancer stem cells
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Pearson Correlation between the expression of CSC transcripts and the transcripts of glucose transporters and the key enzymes involved in glycolysis in ovarian cancer specimens from TCGA and curated from GEPIA. Red indicates significant positive and blue indicates negative correlations.
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3.2. Correlation between OCSCs Markers and Glycolysis
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Table 1
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Pearson Correlation between the expression of CSC transcripts and the transcripts of glucose transporters and the key enzymes involved in glycolysis in ovarian cancer specimens from TCGA and curated from GEPIA. Red indicates significant positive and blue indicates negative correlations.
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[3]
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[7]
CD133
[8]
[9]
ALDH1A1
[10]
[11]
SOX2
[12]
[13]
4-Oct
[14]
[15]
NANOG
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[17]
NOTCH1
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[1] array · 19 items
[0]
[1]
Pearson R
[2]
p-Value
[3]
Pearson R
[4]
p-Value
[5]
Pearson R
[6]
p-Value
[7]
Pearson R
[8]
p-Value
[9]
Pearson R
[10]
p-Value
[11]
Pearson R
[12]
p-Value
[13]
Pearson R
[14]
p-Value
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Pearson R
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p-Value
[17]
Pearson R
[18]
p-Value
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[0]
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0.40
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0.00
[3] array · 19 items
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2.9e−05
[7]
0.14
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0.00
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0.09
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0.07
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0.01
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0.82
[13]
0.11
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0.03
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0.03
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0.60
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0.30
[18]
4.9e−10
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[6]
1.7e−06
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0.42
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0.10
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0.87
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0.22
[18]
2.9e−06
[5] array · 19 items
[0]
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0.02
[7]
−0.04
[8]
0.42
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0.43
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0.01
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0.77
[17]
0.19
[18]
0.00
[6] array · 19 items
[0]
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0.31
[2]
9.7e−11
[3]
−0.02
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0.68
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0.19
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0.00
[7]
0.00
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0.95
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0.15
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0.11
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0.02
[13]
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0.54
[15]
0.03
[16]
0.49
[17]
0.24
[18]
3.3e−07
[7] array · 19 items
[0]
SLC2A4
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[2]
0.77
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0.04
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0.19
[6]
9.4e−05
[7]
0.01
[8]
0.87
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0.00
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0.97
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[18]
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[0]
SLC2A5
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0.06
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0.24
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0.00
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0.98
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0.61
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0.52
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−0.05
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0.29
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0.18
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[2]
5e−07
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0.90
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0.89
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0.00
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0.86
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−0.05
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0.28
[17]
0.29
[18]
1e−09
[10] array · 19 items
[0]
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[3]
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0.82
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0.02
[6]
0.63
[7]
0.02
[8]
0.69
[9]
0.19
[10]
8.7e−05
[11]
0.10
[12]
0.04
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0.04
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0.45
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0.11
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0.04
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6.9e−09
[12] array · 19 items
[0]
LDHA
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3.5e−05
[3]
−0.03
[4]
0.60
[5]
−0.02
[6]
0.74
[7]
−0.03
[8]
0.60
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0.13
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0.06
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0.24
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0.98
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0.24
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3.9e−07
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[0]
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5.4e−06
[16] array · 19 items
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0.15
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0.47
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0.23
[2]
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[3]
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0.86
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0.01
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−0.04
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0.02
[18] array · 19 items
[0]
PHGDH
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0.71
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0.50
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[6]
5.3e−05
[7]
0.10
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0.05
[9]
0.20
[10]
4.8e−05
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0.22
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6.4e−06
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0.30
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section[7]/table-wrap[1]#cancers-12-01267-t001
[4] object · 16 fields
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null
note
Correlation of OCSC markers with TCA enzymes in TCGA. Pearson Correlation between the expression of CSC transcripts and the transcripts of the key TCA enzymes in ovarian cancer specimens from TCGA and curated from GEPIA. Red indicates significant positive, blue indicates negative correlations, and black indicates insignificant p-values of either positive or negative correlations.
structure object · 5 fields
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PMC7281273
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8
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3.3. Correlation between OCSCs Markers and TCA Cycle
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13
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19
table object · 8 fields
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Table 2
caption
Correlation of OCSC markers with TCA enzymes in TCGA. Pearson Correlation between the expression of CSC transcripts and the transcripts of the key TCA enzymes in ovarian cancer specimens from TCGA and curated from GEPIA. Red indicates significant positive, blue indicates negative correlations, and black indicates insignificant p-values of either positive or negative correlations.
rows array · 13 items
[0] array · 19 items
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[3]
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[7]
CD133
[8]
[9]
ALDH1A1
[10]
[11]
SOX2
[12]
[13]
4-Oct
[14]
[15]
NANOG
[16]
[17]
NOTCH1
[18]
[1] array · 19 items
[0]
[1]
Pearson R
[2]
p-Value
[3]
Pearson R
[4]
p-Value
[5]
Pearson R
[6]
p-Value
[7]
Pearson R
[8]
p-Value
[9]
Pearson R
[10]
p-Value
[11]
Pearson R
[12]
p-Value
[13]
Pearson R
[14]
p-Value
[15]
Pearson R
[16]
p-Value
[17]
Pearson R
[18]
p-Value
[2] array · 19 items
[0]
CS
[1]
0.19
[2]
8.2e−05
[3]
0.16
[4]
0.00
[5]
0.23
[6]
9.9e−07
[7]
0.09
[8]
0.06
[9]
0.15
[10]
0.00
[11]
0.00
[12]
0.96
[13]
0.07
[14]
0.18
[15]
0.11
[16]
0.02
[17]
0.39
[18]
0.00
[3] array · 19 items
[0]
ACO1
[1]
0.30
[2]
1.6e−10
[3]
0.08
[4]
0.09
[5]
0.21
[6]
1.1e−05
[7]
0.24
[8]
7.6e−07
[9]
0.30
[10]
5.1e−10
[11]
0.10
[12]
0.05
[13]
0.11
[14]
0.02
[15]
0.00
[16]
0.99
[17]
0.34
[18]
2.8e−13
[4] array · 19 items
[0]
ACO2
[1]
0.18
[2]
0.00
[3]
0.11
[4]
0.02
[5]
−0.06
[6]
0.17
[7]
0.04
[8]
0.41
[9]
−0.03
[10]
0.58
[11]
−0.03
[12]
0.58
[13]
0.10
[14]
0.05
[15]
−0.04
[16]
0.45
[17]
0.24
[18]
3.6e−07
[5] array · 19 items
[0]
IDH1
[1]
0.12
[2]
0.01
[3]
0.08
[4]
0.11
[5]
0.01
[6]
0.77
[7]
0.06
[8]
0.21
[9]
0.16
[10]
0.00
[11]
0.09
[12]
0.08
[13]
0.01
[14]
0.88
[15]
0.02
[16]
0.63
[17]
0.17
[18]
0.00
[6] array · 19 items
[0]
IDH2
[1]
0.16
[2]
0.00
[3]
0.07
[4]
0.13
[5]
0.11
[6]
0.03
[7]
0.07
[8]
0.14
[9]
0.09
[10]
0.08
[11]
0.05
[12]
0.27
[13]
−0.03
[14]
0.51
[15]
0.04
[16]
0.39
[17]
0.25
[18]
2.6e−07
[7] array · 19 items
[0]
IDH3A
[1]
0.16
[2]
0.00
[3]
−0.09
[4]
0.06
[5]
−0.04
[6]
0.44
[7]
0.07
[8]
0.15
[9]
0.09
[10]
0.06
[11]
0.04
[12]
0.37
[13]
−0.03
[14]
0.58
[15]
−0.01
[16]
0.77
[17]
0.24
[18]
4.2e−07
[8] array · 19 items
[0]
IDH3B
[1]
−0.08
[2]
0.12
[3]
0.09
[4]
0.06
[5]
0.09
[6]
0.07
[7]
0.04
[8]
0.48
[9]
0.03
[10]
0.60
[11]
−0.05
[12]
0.35
[13]
0.06
[14]
0.21
[15]
0.04
[16]
0.47
[17]
0.24
[18]
6e−07
[9] array · 19 items
[0]
SUCLG1
[1]
0.13
[2]
0.01
[3]
0.16
[4]
0.00
[5]
0.01
[6]
0.86
[7]
0.01
[8]
0.81
[9]
0.13
[10]
0.01
[11]
0.00
[12]
0.90
[13]
0.00
[14]
0.99
[15]
0.03
[16]
0.50
[17]
0.04
[18]
0.41
[10] array · 19 items
[0]
SUCLG2
[1]
0.19
[2]
9.3e−05
[3]
0.01
[4]
0.89
[5]
−0.08
[6]
0.12
[7]
0.05
[8]
0.27
[9]
0.06
[10]
0.22
[11]
0.08
[12]
0.12
[13]
0.11
[14]
0.02
[15]
0.00
[16]
0.90
[17]
0.05
[18]
0.28
[11] array · 19 items
[0]
MDH2
[1]
0.20
[2]
4.4e−05
[3]
0.00
[4]
0.92
[5]
−0.1
[6]
0.05
[7]
0.00
[8]
0.96
[9]
0.00
[10]
0.97
[11]
0.01
[12]
0.79
[13]
0.07
[14]
0.17
[15]
0.01
[16]
0.87
[17]
0.10
[18]
0.04
[12] array · 19 items
[0]
ME2
[1]
0.27
[2]
9.6e−09
[3]
0.16
[4]
0.00
[5]
0.05
[6]
0.33
[7]
0.08
[8]
0.09
[9]
0.09
[10]
0.07
[11]
0.04
[12]
0.45
[13]
0.13
[14]
0.01
[15]
−0.03
[16]
0.65
[17]
0.12
[18]
0.01
row_count
13
column_count
19
numeric_cells
203
header_rows
2
locator
section[8]/table-wrap[1]#cancers-12-01267-t002
[5] object · 16 fields
id
asset:table:pmid:32429566:3
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:02b3e3c8c267d29c4ce12b15d1f9da6fa6f9befa364cede27fc273a85f8aeb53
bytes
7676
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[9]/table-wrap[1]#cancers-12-01267-t003
version
null
note
Pearson correlation between the expression of CSC transcripts and the transcripts of the key enzymes involved in the ETC in patients’ data curated from TCGA. Red indicates significant positive, blue indicates negative correlations, and black indicates insignificant p-values of either positive or negative correlations.
structure object · 5 fields
pmcid
PMC7281273
section_index
9
section_title
3.4. OXPHOS in Ovarian Cancer Stem Cells
row_count
51
column_count
19
table object · 8 fields
label
Table 3
caption
Pearson correlation between the expression of CSC transcripts and the transcripts of the key enzymes involved in the ETC in patients’ data curated from TCGA. Red indicates significant positive, blue indicates negative correlations, and black indicates insignificant p-values of either positive or negative correlations.
rows array · 51 items
[0] array · 2 items
[0]
TCGA
[1]
[1] array · 19 items
[0]
[1]
CD44
[2]
[3]
CD24
[4]
[5]
CD117
[6]
[7]
CD133
[8]
[9]
ALDH1A1
[10]
[11]
SOX2
[12]
[13]
4-Oct
[14]
[15]
NANOG
[16]
[17]
NOTCH1
[18]
[2] array · 19 items
[0]
Complex I
[1]
Pearson R
[2]
p-Value
[3]
Pearson R
[4]
p-Value
[5]
Pearson R
[6]
p-Value
[7]
Pearson R
[8]
p-Value
[9]
Pearson R
[10]
p-Value
[11]
Pearson R
[12]
p-Value
[13]
Pearson R
[14]
p-Value
[15]
Pearson R
[16]
p-Value
[17]
Pearson R
[18]
p-Value
[3] array · 19 items
[0]
NDUFA10
[1]
0.04
[2]
0.44
[3]
0.02
[4]
0.72
[5]
−0.02
[6]
0.72
[7]
−0.03
[8]
0.52
[9]
0.09
[10]
0.06
[11]
−0.02
[12]
0.62
[13]
−0.03
[14]
0.53
[15]
0.00
[16]
0.93
[17]
0.10
[18]
0.05
[4] array · 19 items
[0]
NDUFA11
[1]
−0.02
[2]
0.62
[3]
0.08
[4]
0.10
[5]
0.00
[6]
0.93
[7]
−0.05
[8]
0.29
[9]
−0.01
[10]
0.86
[11]
−0.02
[12]
0.67
[13]
−0.07
[14]
0.16
[15]
0.05
[16]
0.30
[17]
−0.15
[18]
0.00
[5] array · 19 items
[0]
NDUFAF4
[1]
−0.12
[2]
0.01
[3]
0.23
[4]
1.6e−06
[5]
−0.06
[6]
0.22
[7]
−0.09
[8]
0.05
[9]
0.03
[10]
0.54
[11]
−0.02
[12]
0.76
[13]
0.00
[14]
1.00
[15]
0.05
[16]
0.29
[17]
−0.13
[18]
0.01
[6] array · 19 items
[0]
NDUFA2
[1]
−0.13
[2]
0.01
[3]
−0.03
[4]
0.48
[5]
−0.19
[6]
1e−04
[7]
−0.11
[8]
0.02
[9]
−0.02
[10]
0.66
[11]
−0.02
[12]
0.64
[13]
−0.09
[14]
0.06
[15]
0.01
[16]
0.83
[17]
−0.29
[18]
1.7e−09
[7] array · 19 items
[0]
NDUFB7
[1]
−0.12
[2]
0.01
[3]
−0.02
[4]
0.67
[5]
−0.15
[6]
0.00
[7]
−0.09
[8]
0.06
[9]
−0.05
[10]
0.32
[11]
−0.04
[12]
0.40
[13]
−0.07
[14]
0.15
[15]
0.03
[16]
0.49
[17]
−0.18
[18]
0.00
[8] array · 19 items
[0]
NDUFS1
[1]
0.20
[2]
2.8e−05
[3]
0.16
[4]
0.00
[5]
0.14
[6]
0.00
[7]
0.14
[8]
0.00
[9]
0.17
[10]
0.00
[11]
0.02
[12]
0.69
[13]
0.07
[14]
0.14
[15]
0.03
[16]
0.57
[17]
0.39
[18]
0.00
[9] array · 19 items
[0]
NDUFS2
[1]
0.18
[2]
0.00
[3]
0.13
[4]
0.01
[5]
0.15
[6]
0.00
[7]
0.13
[8]
0.01
[9]
0.06
[10]
0.23
[11]
0.09
[12]
0.06
[13]
0.15
[14]
0.00
[15]
0.16
[16]
0.00
[17]
0.36
[18]
1.3e−14
[10] array · 19 items
[0]
NDUFS3
[1]
0.12
[2]
0.01
[3]
−0.05
[4]
0.29
[5]
−0.12
[6]
0.01
[7]
−0.02
[8]
0.74
[9]
0.00
[10]
0.93
[11]
0.04
[12]
0.39
[13]
0.04
[14]
0.39
[15]
0.02
[16]
0.62
[17]
−0.10
[18]
0.05
[11] array · 19 items
[0]
NDUFS7
[1]
0.15
[2]
0.00
[3]
−0.02
[4]
0.73
[5]
−0.18
[6]
0.00
[7]
−0.08
[8]
0.10
[9]
−0.03
[10]
0.49
[11]
−0.01
[12]
0.89
[13]
−0.01
[14]
0.86
[15]
−0.02
[16]
0.69
[17]
−0.11
[18]
0.02
[12] array · 19 items
[0]
NDUFV1
[1]
0.05
[2]
0.33
[3]
−0.02
[4]
0.71
[5]
−0.13
[6]
0.01
[7]
−0.01
[8]
0.80
[9]
−0.04
[10]
0.43
[11]
0.03
[12]
0.51
[13]
0.18
[14]
0.00
[15]
0.03
[16]
0.61
[17]
0.08
[18]
0.11
[13] array · 19 items
[0]
NDUFV2
[1]
−0.02
[2]
0.71
[3]
0.05
[4]
0.29
[5]
−0.11
[6]
0.02
[7]
0.15
[8]
0.00
[9]
0.02
[10]
0.65
[11]
0.06
[12]
0.18
[13]
−1e−04
[14]
1.00
[15]
0.05
[16]
0.35
[17]
0.01
[18]
0.88
[14] array · 19 items
[0]
NDUFV3
[1]
0.06
[2]
0.24
[3]
−0.01
[4]
0.84
[5]
−0.03
[6]
0.56
[7]
0.07
[8]
0.14
[9]
0.09
[10]
0.07
[11]
0.03
[12]
0.52
[13]
0.10
[14]
0.03
[15]
0.08
[16]
0.10
[17]
0.15
[18]
0.00
[15] array · 2 items
[0]
Complex II
[1]
[16] array · 19 items
[0]
SDHA
[1]
0.11
[2]
0.03
[3]
0.03
[4]
0.52
[5]
−0.04
[6]
0.46
[7]
0.05
[8]
0.35
[9]
0.03
[10]
0.52
[11]
0.11
[12]
0.03
[13]
0.06
[14]
0.20
[15]
0.04
[16]
0.39
[17]
0.16
[18]
0.00
[17] array · 19 items
[0]
SDHB
[1]
0.18
[2]
0.00
[3]
0.09
[4]
0.07
[5]
−0.05
[6]
0.28
[7]
0.05
[8]
0.29
[9]
−0.02
[10]
0.76
[11]
−0.05
[12]
0.29
[13]
0.08
[14]
0.10
[15]
−0.03
[16]
0.56
[17]
0.03
[18]
0.54
[18] array · 19 items
[0]
SDHC
[1]
0.16
[2]
0.00
[3]
0.11
[4]
0.03
[5]
0.10
[6]
0.04
[7]
0.07
[8]
0.15
[9]
0.21
[10]
1.4e−05
[11]
0.06
[12]
0.23
[13]
−0.0029
[14]
0.95
[15]
0.11
[16]
0.03
[17]
0.11
[18]
0.02
[19] array · 19 items
[0]
SDHD
[1]
0.03
[2]
0.59
[3]
0.08
[4]
0.09
[5]
−0.12
[6]
0.01
[7]
0.02
[8]
0.72
[9]
0.00
[10]
0.96
[11]
0.02
[12]
0.75
[13]
0.04
[14]
0.46
[15]
−0.04
[16]
0.43
[17]
−0.03
[18]
0.48
[20] array · 2 items
[0]
Complex III
[1]
[21] array · 19 items
[0]
UQCRB
[1]
−0.12
[2]
0.02
[3]
−0.06
[4]
0.19
[5]
−0.20
[6]
2.6e−05
[7]
−0.08
[8]
0.09
[9]
−0.14
[10]
0.00
[11]
−0.06
[12]
0.20
[13]
−0.1
[14]
0.04
[15]
−0.04
[16]
0.47
[17]
−0.20
[18]
2.1e−05
[22] array · 19 items
[0]
UQCRC1
[1]
0.03
[2]
0.54
[3]
0.08
[4]
0.09
[5]
0.00
[6]
0.94
[7]
0.06
[8]
0.25
[9]
0.08
[10]
0.09
[11]
0.04
[12]
0.39
[13]
0.06
[14]
0.20
[15]
0.13
[16]
0.01
[17]
0.17
[18]
0.00
[23] array · 19 items
[0]
UQCRC2
[1]
0.21
[2]
1.3e−05
[3]
0.17
[4]
0.00
[5]
0.05
[6]
0.31
[7]
0.07
[8]
0.17
[9]
0.00
[10]
0.92
[11]
−0.06
[12]
0.23
[13]
0.15
[14]
0.00
[15]
0.04
[16]
0.37
[17]
0.07
[18]
0.16
[24] array · 19 items
[0]
UQCRH
[1]
−0.04
[2]
0.42
[3]
−0.13
[4]
0.01
[5]
−0.13
[6]
0.01
[7]
−0.01
[8]
0.82
[9]
−0.01
[10]
0.84
[11]
0.00
[12]
1.00
[13]
−0.03
[14]
0.58
[15]
−0.08
[16]
0.12
[17]
−0.17
[18]
0.00
[25] array · 19 items
[0]
UQCRQ
[1]
−0.05
[2]
0.34
[3]
−0.06
[4]
0.20
[5]
−0.17
[6]
0.00
[7]
−0.06
[8]
0.19
[9]
−0.03
[10]
0.60
[11]
−0.02
[12]
0.70
[13]
−0.01
[14]
0.77
[15]
−0.04
[16]
0.41
[17]
−0.31
[18]
3.6e−11
[26] array · 19 items
[0]
UQCR10
[1]
0.04
[2]
0.43
[3]
0.15
[4]
0.00
[5]
−0.1
[6]
0.04
[7]
0.03
[8]
0.50
[9]
0.00
[10]
0.97
[11]
−0.02
[12]
0.70
[13]
0.06
[14]
0.23
[15]
−0.02
[16]
0.66
[17]
−0.11
[18]
0.02
[27] array · 19 items
[0]
UQCR11
[1]
−0.03
[2]
0.57
[3]
−0.05
[4]
0.32
[5]
−0.21
[6]
9.6e−06
[7]
−0.10
[8]
0.04
[9]
−0.07
[10]
0.18
[11]
−0.03
[12]
0.50
[13]
−0.1
[14]
0.04
[15]
−0.03
[16]
0.59
[17]
−0.29
[18]
8e−10
[28] array · 19 items
[0]
CYCS
[1]
0.09
[2]
0.05
[3]
0.07
[4]
0.18
[5]
−0.06
[6]
0.20
[7]
−0.04
[8]
0.43
[9]
0.09
[10]
0.06
[11]
−0.02
[12]
0.73
[13]
0.02
[14]
0.64
[15]
0.03
[16]
0.60
[17]
0.11
[18]
0.03
[29] array · 2 items
[0]
Complex IV
[1]
[30] array · 19 items
[0]
COX4I1
[1]
0.01
[2]
0.81
[3]
0.10
[4]
0.05
[5]
−0.15
[6]
0.00
[7]
0.03
[8]
0.57
[9]
−0.09
[10]
0.07
[11]
−0.06
[12]
0.26
[13]
0.03
[14]
0.50
[15]
−0.06
[16]
0.21
[17]
−0.19
[18]
1e−04
[31] array · 19 items
[0]
COX4I2
[1]
−0.07
[2]
0.18
[3]
0.06
[4]
0.22
[5]
0.25
[6]
2.2e−07
[7]
0.01
[8]
0.83
[9]
0.17
[10]
0.00
[11]
−0.01
[12]
0.82
[13]
−0.08
[14]
0.10
[15]
0.16
[16]
0.00
[17]
0.15
[18]
0.00
[32] array · 19 items
[0]
COX5A
[1]
0.00
[2]
0.95
[3]
−0.09
[4]
0.08
[5]
−0.19
[6]
9.3e−05
[7]
−0.04
[8]
0.42
[9]
0.00
[10]
0.95
[11]
−0.04
[12]
0.43
[13]
−0.04
[14]
0.42
[15]
−0.05
[16]
0.31
[17]
−0.13
[18]
0.01
[33] array · 19 items
[0]
COX5B
[1]
−0.22
[2]
6.6e−06
[3]
0.10
[4]
0.04
[5]
−0.18
[6]
0.00
[7]
−0.07
[8]
0.13
[9]
−0.09
[10]
0.08
[11]
−0.02
[12]
0.64
[13]
−0.02
[14]
0.68
[15]
−0.04
[16]
0.36
[17]
−0.27
[18]
1.7e−08
[34] array · 19 items
[0]
COX6A1
[1]
−0.1
[2]
0.04
[3]
0.03
[4]
0.53
[5]
−0.11
[6]
0.03
[7]
−0.06
[8]
0.23
[9]
0.07
[10]
0.13
[11]
0.01
[12]
0.87
[13]
−0.10
[14]
0.04
[15]
0.06
[16]
0.19
[17]
−0.12
[18]
0.02
[35] array · 19 items
[0]
COX6A2
[1]
−0.13
[2]
0.01
[3]
0.09
[4]
0.06
[5]
0.20
[6]
3.1e−05
[7]
0.00
[8]
0.92
[9]
0.14
[10]
0.00
[11]
0.02
[12]
0.69
[13]
−0.07
[14]
0.14
[15]
0.24
[16]
3.6e−07
[17]
0.04
[18]
0.39
[36] array · 19 items
[0]
COX6B1
[1]
−0.06
[2]
0.21
[3]
−0.03
[4]
0.61
[5]
−0.02
[6]
0.73
[7]
−0.06
[8]
0.23
[9]
0.07
[10]
0.15
[11]
−0.01
[12]
0.87
[13]
0.01
[14]
0.85
[15]
0.07
[16]
0.15
[17]
−0.19
[18]
0.00
[37] array · 19 items
[0]
COX6B2
[1]
−0.04
[2]
0.38
[3]
−0.01
[4]
0.77
[5]
0.06
[6]
0.20
[7]
−0.03
[8]
0.54
[9]
0.00
[10]
0.94
[11]
−0.03
[12]
0.48
[13]
0.00
[14]
0.96
[15]
0.07
[16]
0.15
[17]
0.23
[18]
2.6e−06
[38] array · 19 items
[0]
COX6C
[1]
−0.09
[2]
0.05
[3]
−0.12
[4]
0.01
[5]
−0.20
[6]
5e−05
[7]
−0.032
[8]
0.51
[9]
−0.13
[10]
0.01
[11]
−0.04
[12]
0.39
[13]
−0.12
[14]
0.01
[15]
−0.01
[16]
0.91
[17]
−0.12
[18]
0.01
[39] array · 19 items
[0]
COX7A1
[1]
−0.02
[2]
0.64
[3]
−0.06
[4]
0.24
[5]
0.13
[6]
0.01
[7]
−0.03
[8]
0.56
[9]
0.08
[10]
0.09
[11]
−0.04
[12]
0.38
[13]
−0.06
[14]
0.19
[15]
0.02
[16]
0.67
[17]
0.00
[18]
0.99
[40] array · 19 items
[0]
COX7A2
[1]
−0.08
[2]
0.09
[3]
0.09
[4]
0.05
[5]
−0.04
[6]
0.40
[7]
−0.09
[8]
0.06
[9]
0.02
[10]
0.74
[11]
0.00
[12]
0.93
[13]
−0.08
[14]
0.09
[15]
0.01
[16]
0.87
[17]
−0.19
[18]
5.8e−05
[41] array · 19 items
[0]
COX7B
[1]
−0.02
[2]
0.70
[3]
−0.01
[4]
0.78
[5]
−0.19
[6]
1e−04
[7]
−0.07
[8]
0.14
[9]
0.01
[10]
0.78
[11]
0.00
[12]
0.95
[13]
−0.07
[14]
0.15
[15]
0.00
[16]
0.98
[17]
−0.27
[18]
1.1e−08
[42] array · 19 items
[0]
COX7C
[1]
−0.21
[2]
9.9e−06
[3]
0.03
[4]
0.55
[5]
−0.08
[6]
0.09
[7]
−0.09
[8]
0.08
[9]
−0.10
[10]
0.04
[11]
−0.09
[12]
0.06
[13]
0.00
[14]
0.96
[15]
−0.01
[16]
0.84
[17]
−0.30
[18]
2.8e−10
[43] array · 2 items
[0]
Complex V
[1]
[44] array · 19 items
[0]
ATP5C1
[1]
0.03
[2]
0.51
[3]
0.08
[4]
0.11
[5]
−0.06
[6]
0.24
[7]
−0.06
[8]
0.22
[9]
−0.02
[10]
0.62
[11]
0.01
[12]
0.87
[13]
−0.05
[14]
0.36
[15]
−0.05
[16]
0.28
[17]
−0.07
[18]
0.13
[45] array · 19 items
[0]
ATP5D
[1]
−0.02
[2]
0.63
[3]
−0.01
[4]
0.91
[5]
−0.22
[6]
7.6e−06
[7]
−0.11
[8]
0.02
[9]
−0.15
[10]
0.00
[11]
−0.06
[12]
0.26
[13]
0.00
[14]
0.93
[15]
−0.04
[16]
0.38
[17]
−0.18
[18]
0.00
[46] array · 19 items
[0]
ATP5E
[1]
−0.14
[2]
0.00
[3]
0.00
[4]
0.93
[5]
−0.05
[6]
0.33
[7]
−0.03
[8]
0.54
[9]
0.03
[10]
0.52
[11]
0.06
[12]
0.26
[13]
−0.10
[14]
0.04
[15]
0.02
[16]
0.76
[17]
−0.19
[18]
0.00
[47] array · 19 items
[0]
ATP5G3
[1]
0.07
[2]
0.14
[3]
−0.04
[4]
0.36
[5]
−0.16
[6]
0.00
[7]
−0.08
[8]
0.08
[9]
−0.01
[10]
0.87
[11]
−0.06
[12]
0.23
[13]
−0.05
[14]
0.34
[15]
−0.07
[16]
0.17
[17]
−0.13
[18]
0.01
[48] array · 19 items
[0]
ATP5J
[1]
−0.03
[2]
0.52
[3]
−0.02
[4]
0.65
[5]
−0.10
[6]
0.05
[7]
−0.04
[8]
0.44
[9]
0.17
[10]
0.00
[11]
−0.01
[12]
0.84
[13]
0.01
[14]
0.89
[15]
0.00
[16]
0.97
[17]
−0.17
[18]
0.00
[49] array · 19 items
[0]
ATP5O
[1]
−0.10
[2]
0.04
[3]
−0.02
[4]
0.75
[5]
−0.10
[6]
0.03
[7]
−0.06
[8]
0.23
[9]
−0.07
[10]
0.14
[11]
−0.07
[12]
0.14
[13]
0.06
[14]
0.25
[15]
0.04
[16]
0.46
[17]
−0.19
[18]
0.00
[50] array · 19 items
[0]
ATP5S
[1]
0.02
[2]
0.71
[3]
0.00
[4]
0.99
[5]
0.08
[6]
0.10
[7]
0.10
[8]
0.03
[9]
0.14
[10]
0.00
[11]
−0.01
[12]
0.78
[13]
0.05
[14]
0.32
[15]
0.13
[16]
0.01
[17]
0.10
[18]
0.04
row_count
51
column_count
19
numeric_cells
801
header_rows
3
locator
section[9]/table-wrap[1]#cancers-12-01267-t003
[6] object · 16 fields
id
asset:table:pmid:32429566:4
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:c09953c5c5be5e51d6f3c69469e1f975b6280fb5b29bbb34255f7d8c338a7ff0
bytes
2163
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[10]/table-wrap[1]#cancers-12-01267-t004
version
null
note
Correlation between OCSC markers and lipid transporters and key enzymes in lipid metabolism in TCGA. Red indicates significant positive, and black indicates insignificant p-values of either positive or negative correlations.
structure object · 5 fields
pmcid
PMC7281273
section_index
10
section_title
3.5. Correlation of OCSC Markers With Lipid Metabolism
row_count
12
column_count
19
table object · 8 fields
label
Table 4
caption
Correlation between OCSC markers and lipid transporters and key enzymes in lipid metabolism in TCGA. Red indicates significant positive, and black indicates insignificant p-values of either positive or negative correlations.
rows array · 12 items
[0] array · 19 items
[0]
TCGA
[1]
CD44
[2]
[3]
CD24
[4]
[5]
CD117
[6]
[7]
CD133
[8]
[9]
ALDH1A1
[10]
[11]
SOX2
[12]
[13]
4-Oct
[14]
[15]
NANOG
[16]
[17]
NOTCH1
[18]
[1] array · 19 items
[0]
[1]
Pearson R
[2]
p-Value
[3]
Pearson R
[4]
p-Value
[5]
Pearson R
[6]
p-Value
[7]
Pearson R
[8]
p-Value
[9]
Pearson R
[10]
p-Value
[11]
Pearson R
[12]
p-Value
[13]
Pearson R
[14]
p-Value
[15]
Pearson R
[16]
p-Value
[17]
Pearson R
[18]
p-Value
[2] array · 19 items
[0]
FABP4
[1]
0.04
[2]
0.43
[3]
−0.04
[4]
0.44
[5]
0.05
[6]
0.28
[7]
−0.07
[8]
0.13
[9]
0.05
[10]
0.33
[11]
−0.04
[12]
0.43
[13]
0.00
[14]
0.87
[15]
−0.06
[16]
0.21
[17]
0.07
[18]
0.13
[3] array · 19 items
[0]
CD36
[1]
0.17
[2]
0.00
[3]
−0.02
[4]
0.63
[5]
0.11
[6]
0.02
[7]
−0.07
[8]
0.14
[9]
0.09
[10]
0.07
[11]
0.03
[12]
0.51
[13]
−0.03
[14]
0.55
[15]
0.00
[16]
0.90
[17]
0.24
[18]
4e−07
[4] array · 19 items
[0]
ACLY
[1]
0.21
[2]
9e−06
[3]
0.13
[4]
0.01
[5]
0.37
[6]
3.1e−15
[7]
0.21
[8]
1.8e−05
[9]
0.15
[10]
0.00
[11]
0.04
[12]
0.43
[13]
0.01
[14]
0.85
[15]
0.12
[16]
0.02
[17]
0.51
[18]
0.00
[5] array · 19 items
[0]
ACACA
[1]
0.16
[2]
0.00
[3]
0.20
[4]
3.1e−05
[5]
0.19
[6]
0.00
[7]
0.22
[8]
4.5e−06
[9]
0.10
[10]
0.03
[11]
0.01
[12]
0.79
[13]
0.08
[14]
0.11
[15]
0.02
[16]
0.73
[17]
0.32
[18]
6.3e−12
[6] array · 19 items
[0]
ACACB
[1]
0.10
[2]
0.04
[3]
0.00
[4]
0.99
[5]
0.27
[6]
1.7e−08
[7]
0.11
[8]
0.02
[9]
0.13
[10]
0.01
[11]
0.03
[12]
0.58
[13]
0.10
[14]
0.04
[15]
0.12
[16]
0.02
[17]
0.40
[18]
0.00
[7] array · 19 items
[0]
CPT1A
[1]
0.12
[2]
0.01
[3]
0.03
[4]
0.56
[5]
0.11
[6]
0.02
[7]
0.16
[8]
0.00
[9]
0.09
[10]
0.07
[11]
0.06
[12]
0.20
[13]
0.09
[14]
0.07
[15]
0.00
[16]
0.89
[17]
0.35
[18]
7.1e−14
[8] array · 19 items
[0]
CPT1B
[1]
0.16
[2]
0.00
[3]
−0.07
[4]
0.15
[5]
−0.05
[6]
0.30
[7]
−0.02
[8]
0.64
[9]
0.00
[10]
0.93
[11]
0.12
[12]
0.02
[13]
0.13
[14]
0.01
[15]
0.08
[16]
0.11
[17]
0.17
[18]
3e−04
[9] array · 19 items
[0]
CPT2
[1]
0.19
[2]
7.7e−05
[3]
0.03
[4]
0.57
[5]
0.08
[6]
0.08
[7]
0.18
[8]
0.00
[9]
0.18
[10]
0.00
[11]
0.09
[12]
0.06
[13]
0.06
[14]
0.20
[15]
0.09
[16]
0.07
[17]
0.29
[18]
7.1e−10
[10] array · 19 items
[0]
FASN
[1]
0.08
[2]
0.08
[3]
0.06
[4]
0.25
[5]
0.10
[6]
0.03
[7]
0.05
[8]
0.31
[9]
0.05
[10]
0.28
[11]
0.00
[12]
0.85
[13]
−0.02
[14]
0.66
[15]
0.02
[16]
0.67
[17]
0.42
[18]
0.00
[11] array · 19 items
[0]
SCD1
[1]
0.27
[2]
1.3e−08
[3]
0.06
[4]
0.20
[5]
0.11
[6]
0.02
[7]
0.08
[8]
0.10
[9]
0.08
[10]
0.12
[11]
0.11
[12]
0.03
[13]
−0.05
[14]
0.28
[15]
−0.02
[16]
0.67
[17]
0.27
[18]
1.5e−08
row_count
12
column_count
19
numeric_cells
186
header_rows
2
locator
section[10]/table-wrap[1]#cancers-12-01267-t004
[7] object · 16 fields
id
asset:table:pmid:32429566:5
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:31b381770795ed5f0ac12b44026fa7062da3fe04a91f903c2486f7145e0aa874
bytes
2233
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[11]/table-wrap[1]#cancers-12-01267-t005
version
null
note
Correlation between OCSC markers and glutamate transporters and key enzymes in glutamate/glutamine metabolism in TCGA. Red indicates significant positive and black indicates insignificant p-values of either positive or negative correlations.
structure object · 5 fields
pmcid
PMC7281273
section_index
11
section_title
3.6. Glutamine/Glutamate Metabolism in OCSCs
row_count
12
column_count
19
table object · 8 fields
label
Table 5
caption
Correlation between OCSC markers and glutamate transporters and key enzymes in glutamate/glutamine metabolism in TCGA. Red indicates significant positive and black indicates insignificant p-values of either positive or negative correlations.
rows array · 12 items
[0] array · 19 items
[0]
TCGA
[1]
CD44
[2]
[3]
CD24
[4]
[5]
CD117
[6]
[7]
CD133
[8]
[9]
ALDH1A1
[10]
[11]
SOX2
[12]
[13]
4-Oct
[14]
[15]
NANOG
[16]
[17]
NOTCH1
[18]
[1] array · 19 items
[0]
[1]
Pearson R
[2]
p-Value
[3]
Pearson R
[4]
p-Value
[5]
Pearson R
[6]
p-Value
[7]
Pearson R
[8]
p-Value
[9]
Pearson R
[10]
p-Value
[11]
Pearson R
[12]
p-Value
[13]
Pearson R
[14]
p-Value
[15]
Pearson R
[16]
p-Value
[17]
Pearson R
[18]
p-Value
[2] array · 19 items
[0]
SLC1A1
[1]
0.32
[2]
1.2e−11
[3]
0.10
[4]
0.05
[5]
0.04
[6]
0.39
[7]
0.20
[8]
3.9e−05
[9]
0.12
[10]
0.01
[11]
0.15
[12]
0.00
[13]
0.18
[14]
0.00
[15]
−0.04
[16]
0.40
[17]
0.09
[18]
0.06
[3] array · 19 items
[0]
SLC1A2
[1]
0.16
[2]
0.00
[3]
0.00
[4]
0.93
[5]
0.25
[6]
1e−07
[7]
0.12
[8]
0.01
[9]
0.22
[10]
4.1e−06
[11]
0.05
[12]
0.31
[13]
0.04
[14]
0.44
[15]
0.07
[16]
0.13
[17]
0.14
[18]
0.00
[4] array · 19 items
[0]
SLC1A3
[1]
0.20
[2]
4.6e−05
[3]
0.08
[4]
0.12
[5]
0.09
[6]
0.08
[7]
0.18
[8]
0.00
[9]
−0.04
[10]
0.47
[11]
0.08
[12]
0.11
[13]
0.20
[14]
4.8e−05
[15]
−0.01
[16]
0.82
[17]
0.15
[18]
0.00
[5] array · 19 items
[0]
SLC1A4
[1]
0.27
[2]
1.5e−08
[3]
−0.03
[4]
0.60
[5]
0.27
[6]
1.8e−08
[7]
0.13
[8]
0.01
[9]
0.25
[10]
2.3e−07
[11]
0.11
[12]
0.02
[13]
0.00
[14]
0.99
[15]
0.09
[16]
0.06
[17]
0.36
[18]
1.4e−14
[6] array · 19 items
[0]
SLC1A5
[1]
0.24
[2]
3.7e−07
[3]
−0.08
[4]
0.10
[5]
0.06
[6]
0.21
[7]
0.03
[8]
0.56
[9]
0.05
[10]
0.35
[11]
0.15
[12]
0.00
[13]
0.03
[14]
0.50
[15]
−0.03
[16]
0.58
[17]
0.22
[18]
7.4e−06
[7] array · 19 items
[0]
SLC1A6
[1]
−0.02
[2]
0.64
[3]
0.02
[4]
0.76
[5]
0.03
[6]
0.53
[7]
0.02
[8]
0.69
[9]
0.00
[10]
0.96
[11]
0.01
[12]
0.78
[13]
−0.04
[14]
0.38
[15]
0.06
[16]
0.21
[17]
0.04
[18]
0.40
[8] array · 19 items
[0]
SLC1A7
[1]
0.09
[2]
0.08
[3]
−0.06
[4]
0.21
[5]
0.43
[6]
0.00
[7]
0.25
[8]
2.4e−07
[9]
0.16
[10]
0.00
[11]
−0.05
[12]
0.35
[13]
−0.03
[14]
0.50
[15]
−0.04
[16]
0.47
[17]
0.33
[18]
2e−12
[9] array · 19 items
[0]
GLS
[1]
0.15
[2]
0.00
[3]
−0.01
[4]
0.86
[5]
0.11
[6]
0.02
[7]
−0.01
[8]
0.86
[9]
0.18
[10]
0.00
[11]
0.03
[12]
0.49
[13]
0.05
[14]
0.30
[15]
0.13
[16]
0.01
[17]
0.36
[18]
2.8e−14
[10] array · 19 items
[0]
GLUD1
[1]
0.10
[2]
0.03
[3]
0.02
[4]
0.73
[5]
0.11
[6]
0.03
[7]
0.06
[8]
0.20
[9]
0.11
[10]
0.02
[11]
−0.02
[12]
0.68
[13]
0.14
[14]
0.00
[15]
0.05
[16]
0.35
[17]
0.25
[18]
2.2e−07
[11] array · 19 items
[0]
GLUD2
[1]
0.19
[2]
7.8e−05
[3]
0.04
[4]
0.73
[5]
0.25
[6]
2.6e−07
[7]
0.05
[8]
0.31
[9]
0.26
[10]
4.8e−08
[11]
0.09
[12]
0.08
[13]
0.15
[14]
0.00
[15]
0.31
[16]
9.3e−11
[17]
0.27
[18]
1.3e−08
row_count
12
column_count
19
numeric_cells
185
header_rows
2
locator
section[11]/table-wrap[1]#cancers-12-01267-t005
gaps array · 4 items
[0]
asset:data:geo:GSE28799 not downloaded
[1]
asset:data:geo:GSE28799 licence not read
[2]
asset:data:geo:GSE64999 not downloaded
[3]
asset:data:geo:GSE64999 licence not read
analysis object · 4 fields
state
partial
methods array · 2 items
[0] object · 10 fields
id
method-1
family
correlation_analysis
specific
pearson
label
Correlation analysis
dsl_operations array · 1 item
[0]
pearson_r
missing_operations array · 0 items
expressible
true
parameters object · 0 fields
data_shapes array · 1 item
[0]
paired_numeric_columns
evidence object · 3 fields
score
0.8
band
high
quote
Pearson Correlation
[1] object · 10 fields
id
method-2
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null
specific
null
label
multiple t-test with Holm–Sidak method
dsl_operations array · 0 items
missing_operations array · 0 items
expressible
null
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
score
1
band
verbatim
quote
The differential expression of the OCSCs markers and the enzymes involved in the metabolic pathways in OCSCs and their parental cells was analyzed by the multiple t-test with Holm–Sidak method, and each gene was analyzed individually between the two groups, without assuming a consistent SD with p ≤ 0.05.
targets array · 0 items
gaps array · 1 item
[0]
method.reader_named_unmapped
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
availability_state
owned
tier_unlocked
R1
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocking_axis
none
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 1 item
[0]
pearson_r
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pearson.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R1
reachable
true
accessions array · 2 items
[0]
GSE28799
[1]
GSE64999
resolved_accessions array · 2 items
[0]
GSE28799
[1]
GSE64999
statements array · 1 item
[0]
Gene expression profiles of two studies of OCSC GSE28799 [41] and GSE64999 [42] with platform information of GPL570 and GPL17077, respectively, were extracted from Gene Expression Omnibus (GEO). Both included ovarian cancer spheroids and their parental cells. GSE28799 included OVCAR3-derived spheroids and their parental OVCAR3 in triplicates.
basis
The paper names GSE28799, GSE64999 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 1 item
[0]
pearson_r
assets array · 7 items
[0]
source:pmid:32429566
[1]
data:geo:GSE28799
[2]
asset:table:pmid:32429566:1
[3]
asset:table:pmid:32429566:2
[4]
asset:table:pmid:32429566:3
[5]
asset:table:pmid:32429566:4
[6]
asset:table:pmid:32429566:5
steps array · 1 item
[0]
run_analysis
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE28799
gaps array · 0 items
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-10-31T18:20:06Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
null
calls
3
usage object · 3 fields
prompt_tokens
57818
completion_tokens
2344
cached_tokens
784
human_critique
null
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
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MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
execution object · 5 fields
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absent
status
not_run
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null
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gaps array · 1 item
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execution.not_run
provenance object · 7 fields
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pmid:32429566
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paper
label
pmid:32429566
[1] object · 3 fields
id
source:pmid:32429566
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manuscript
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PMID 32429566 full text
[2] object · 3 fields
id
data:geo:GSE28799
type
dataset
label
GEO GSE28799
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:32429566
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paper
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pmid:32429566
[1] object · 3 fields
id
source:pmid:32429566
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manuscript
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PMID 32429566 full text
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id
data:geo:GSE28799
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dataset
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GEO GSE28799
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-32429566
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extraction
used array · 1 item
[0]
source:pmid:32429566
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE28799
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accession_resolution
used array · 1 item
[0]
data:geo:GSE28799
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
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software
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Corpus assay engine
[1] object · 3 fields
id
agent:minimax-reader
type
software
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MiniMax literature reader
source_run_id
reading-sci-2026-11-01
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
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ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:32429566
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sha256:96e2b62e1274cf4fa9f8107eb06bf79dc35de16627281c172b848a74e40af59a
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null
generation
6
gaps array · 9 items
[0]
asset:data:geo:GSE28799 licence not read
[1]
asset:data:geo:GSE28799 not downloaded
[2]
asset:data:geo:GSE64999 licence not read
[3]
asset:data:geo:GSE64999 not downloaded
[4]
execution.not_run
[5]
method.reader_named_unmapped
[6]
review.human_critique
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review.independent_reader
[8]
review.machine_critique
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[0] object · 11 fields
role
analysis
definition_id
correlation_analysis
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f2132e96ae6c7a4e
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null
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pearson_r
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supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
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0.8
evidence array · 1 item
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Pearson Correlation
order_basis
analysis_only
id
assay:1
Complete file 
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32429566", "kind": "science-record", "revision": 7, "content_hash": "sha256:018e2d7bf936931e3006cfc526e8c2ee1cc07a0ee5d21d5dd7d898dbc65d101d", "created_at": "2026-11-01T15:41:02Z", "updated_at": "2026-11-01T21:23:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Metabolic Plasticity in Ovarian Cancer Stem Cells.", "doi": "10.3390/cancers12051267", "pmid": "32429566", "authors": ["Alia Ghoneum", "Daniela Gonzalez", "Ammar Yasser Abdulfattah", "Neveen Said"], "journal": "Cancers", "year": 2020, "abstract": "Ovarian Cancer is the fifth most common cancer in females and remains the most lethal gynecological malignancy as most patients are diagnosed at late stages of the disease. Despite initial responses to therapy, recurrence of chemo-resistant disease is common. The presence of residual cancer stem cells (CSCs) with the unique ability to adapt to several metabolic and signaling pathways represents a major challenge in developing novel targeted therapies. The objective of this study is to investigate the transcripts of putative ovarian cancer stem cell (OCSC) markers in correlation with transcripts of receptors, transporters, and enzymes of the energy generating metabolic pathways involved in high grade serous ovarian cancer (HGSOC). We conducted correlative analysis in data downloaded from The Cancer Genome Atlas (TCGA), studies of experimental OCSCs and their parental lines from Gene Expression Omnibus (GEO), and Cancer Cell Line Encyclopedia (CCLE). We found positive correlations between the transcripts of OCSC markers, specifically CD44, and glycolytic markers. TCGA datasets revealed that NOTCH1, CD133, CD44, CD24, and ALDH1A1, positively and significantly correlated with tricarboxylic acid cycle (TCA) enzymes. OVCAR3-OCSCs (cancer stem cells derived from a well-established epithelial ovarian cancer cell line) exhibited enrichment of the electron transport chain (ETC) mainly in complexes I, III, IV, and V, further supporting reliance on the oxidative phosphorylation (OXPHOS) phenotype. OVCAR3-OCSCs also exhibited significant increase in CD36, ACACA, SCD, and CPT1A, with CD44, CD133, and ALDH1A1 exhibiting positive correlations with lipid metabolic enzymes. TCGA data show positive correlations between OCSC markers and glutamine metabolism enzymes, whereas in OCSC experimental models of GSE64999, GSE28799, and CCLE, the number of positive and negative correlations observed was significantly lower and was different between model systems. Appropriate integration and validation of data model systems with those in patients' specimens is needed not only to bridge our knowledge gap of metabolic programing of OCSCs, but also in designing novel strategies to target the metabolic plasticity of dormant, resistant, and CSCs.", "claims": [{"id": "claim-method", "statement": "The differential expression of the OCSCs markers and the enzymes involved in the metabolic pathways in OCSCs and their parental cells was analyzed by the multiple t-test with Holm–Sidak method, and each gene was analyzed individually between the two groups, without assuming a consistent SD with p ≤ 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32429566", "locator": "sections[4] \"2.2. 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Microarray Extraction\" paragraph 2", "quote": "Gene expression profiles of two studies of OCSC GSE28799 [41] and GSE64999 [42] with platform information of GPL570 and GPL17077, respectively, were extracted from Gene Expression Omnibus (GEO). Both included ovarian cancer spheroids and their parental cells. GSE28799 included OVCAR3-derived spheroids and their parental OVCAR3 in triplicates."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:32429566"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE28799"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE28799"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32429566", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/cancers12051267", "sha256": "sha256:55af975f75c16e5bae97d2ec89b8ae412c30e9ef1ace895aa799a41095719032", "bytes": 75683, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/cancers12051267", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7281273", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE28799", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28799", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28799", "version": null, "note": "Gene expression profiles of two studies of OCSC GSE28799 [41] and GSE64999 [42] with platform information of GPL570 and GPL17077, respectively, were extracted from Gene Expression Omnibus (GEO). 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GSE28799 included OVCAR3-derived spheroids and their parental OVCAR3 in triplicates.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM713222", "GSM713223", "GSM713224", "GSM713227", "GSM713228", "GSM713229"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Isolation and characterization of stem-like cells from a human ovarian cancer cell line", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE64999", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64999", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE64999", "version": null, "note": "Gene expression profiles of two studies of OCSC GSE28799 [41] and GSE64999 [42] with platform information of GPL570 and GPL17077, respectively, were extracted from Gene Expression Omnibus (GEO). 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GSE28799 included OVCAR3-derived spheroids and their parental OVCAR3 in triplicates.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1585598", "GSM1585599", "GSM1585600", "GSM1585601", "GSM1585602", "GSM1585603", "GSM1585604", "GSM1585605"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "17077", "taxon": "Homo sapiens", "title": "Gene regulation during differentiation of ovarian cancer stem cells", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32429566:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a431c114b601779f24d23d1936999b62f4daf0b9731dd772a94fa3d865e0dd5d", "bytes": 3258, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#cancers-12-01267-t001", "version": null, "note": "Pearson Correlation between the expression of CSC transcripts and the transcripts of glucose transporters and the key enzymes involved in glycolysis in ovarian cancer specimens from TCGA and curated from GEPIA. Red indicates significant positive and blue indicates negative correlations.", "structure": {"pmcid": "PMC7281273", "section_index": 7, "section_title": "3.2. Correlation between OCSCs Markers and Glycolysis", "row_count": 19, "column_count": 19}, "table": {"label": "Table 1", "caption": "Pearson Correlation between the expression of CSC transcripts and the transcripts of glucose transporters and the key enzymes involved in glycolysis in ovarian cancer specimens from TCGA and curated from GEPIA. Red indicates significant positive and blue indicates negative correlations.", "rows": [["TCGA", "CD44", "", "CD24", "", "CD117", "", "CD133", "", "ALDH1A1", "", "SOX2", "", "4-Oct", "", "NANOG", "", "NOTCH1", ""], ["", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value"], ["HK1", "0.29", "0.00", "7e−04", "0.99", "0.15", "0.00", "0.14", "0.00", "0.13", "0.01", "0.03", "0.60", "0.03", "0.61", "0.06", "0.25", "0.40", "0.00"], ["HK2", "0.13", "0.01", "0.09", "0.08", "0.20", "2.9e−05", "0.14", "0.00", "0.09", "0.07", "0.01", "0.82", "0.11", "0.03", "0.03", "0.60", "0.30", "4.9e−10"], ["SLC2A1", "0.09", "0.07", "0.00", "0.95", "0.23", "1.7e−06", "0.04", "0.42", "0.10", "0.03", "0.00", "0.87", "0.00", "0.95", "0.03", "0.60", "0.22", "2.9e−06"], ["SLC2A2", "0.07", "0.16", "−0.03", "0.60", "0.12", "0.02", "−0.04", "0.42", "0.08", "0.09", "−0.03", "0.48", "−0.04", "0.43", "0.01", "0.77", "0.19", "0.00"], ["SLC2A3", "0.31", "9.7e−11", "−0.02", "0.68", "0.19", "0.00", "0.00", "0.95", "0.07", "0.15", "0.11", "0.02", "−0.03", "0.54", "0.03", "0.49", "0.24", "3.3e−07"], ["SLC2A4", "0.01", "0.77", "0.04", "0.37", "0.19", "9.4e−05", "0.01", "0.87", "0.00", "0.97", "0.09", "0.06", "0.01", "0.77", "0.09", "0.06", "0.18", "0.00"], ["SLC2A5", "0.45", "0.00", "0.02", "0.74", "0.06", "0.24", "0.00", "0.98", "−0.03", "0.61", "−0.03", "0.57", "0.03", "0.52", "−0.05", "0.29", "0.18", "0.00"], ["SLC2A6", "0.24", "5e−07", "−0.12", "0.01", "0.00", "0.90", "0.00", "0.89", "0.05", "0.31", "0.00", "0.86", "−0.04", "0.40", "−0.05", "0.28", "0.29", "1e−09"], ["PGK1", "0.30", "4.4 × 1010", "−0.01", "0.82", "0.02", "0.63", "0.02", "0.69", "0.19", "8.7e−05", "0.10", "0.04", "0.00", "1.00", "0.04", "0.45", "0.14", "0.00"], ["PFKFB3", "0.35", "0.00", "0.00", "0.93", "0.11", "0.02", "0.11", "0.03", "0.04", "0.39", "0.10", "0.03", "0.09", "0.07", "−0.01", "0.77", "0.28", "6.9e−09"], ["LDHA", "0.20", "3.5e−05", "−0.03", "0.60", "−0.02", "0.74", "−0.03", "0.60", "0.13", "0.01", "0.06", "0.24", "0.04", "0.46", "0.00", "0.97", "−0.02", "0.65"], ["FBP1", "0.40", "0.00", "−0.11", "0.02", "−0.06", "0.24", "0.00", "0.98", "0.11", "0.03", "0.06", "0.19", "0.00", "0.96", "0.00", "0.93", "0.03", "0.48"], ["PDK1", "0.12", "0.01", "0.02", "0.66", "0.04", "0.38", "0.06", "0.23", "0.24", "3.9e−07", "0.04", "0.41", "0.04", "0.42", "0.01", "0.80", "0.13", "0.01"], ["PDHA", "0.12", "0.01", "−0.02", "0.75", "−0.02", "0.70", "0.07", "0.13", "0.14", "0.01", "0.09", "0.06", "0.08", "0.11", "0.03", "0.51", "0.22", "5.4e−06"], ["TPI1", "0.07", "0.15", "0.05", "0.33", "−0.04", "0.47", "−0.06", "0.25", "0.03", "0.56", "0.02", "0.75", "−0.01", "0.77", "0.08", "0.10", "−0.02", "0.74"], ["ENO1", "0.23", "1.3e−06", "0.07", "0.17", "−0.02", "0.71", "0.09", "0.08", "0.10", "0.05", "0.01", "0.86", "0.13", "0.01", "−0.04", "0.47", "0.12", "0.02"], ["PHGDH", "0.02", "0.71", "0.03", "0.50", "0.19", "5.3e−05", "0.10", "0.05", "0.20", "4.8e−05", "0.22", "6.4e−06", "−0.05", "0.30", "0.14", "0.00", "0.14", "0.00"]], "row_count": 19, "column_count": 19, "numeric_cells": 311, "header_rows": 2, "locator": "section[7]/table-wrap[1]#cancers-12-01267-t001"}}, {"id": "asset:table:pmid:32429566:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e9b781092a3c2cc32c247abbbc02a919cef3cddd99bd0d0393cdfb7fef719b92", "bytes": 2459, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#cancers-12-01267-t002", "version": null, "note": "Correlation of OCSC markers with TCA enzymes in TCGA. Pearson Correlation between the expression of CSC transcripts and the transcripts of the key TCA enzymes in ovarian cancer specimens from TCGA and curated from GEPIA. Red indicates significant positive, blue indicates negative correlations, and black indicates insignificant p-values of either positive or negative correlations.", "structure": {"pmcid": "PMC7281273", "section_index": 8, "section_title": "3.3. Correlation between OCSCs Markers and TCA Cycle", "row_count": 13, "column_count": 19}, "table": {"label": "Table 2", "caption": "Correlation of OCSC markers with TCA enzymes in TCGA. Pearson Correlation between the expression of CSC transcripts and the transcripts of the key TCA enzymes in ovarian cancer specimens from TCGA and curated from GEPIA. Red indicates significant positive, blue indicates negative correlations, and black indicates insignificant p-values of either positive or negative correlations.", "rows": [["TCGA", "CD44", "", "CD24", "", "CD117", "", "CD133", "", "ALDH1A1", "", "SOX2", "", "4-Oct", "", "NANOG", "", "NOTCH1", ""], ["", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value"], ["CS", "0.19", "8.2e−05", "0.16", "0.00", "0.23", "9.9e−07", "0.09", "0.06", "0.15", "0.00", "0.00", "0.96", "0.07", "0.18", "0.11", "0.02", "0.39", "0.00"], ["ACO1", "0.30", "1.6e−10", "0.08", "0.09", "0.21", "1.1e−05", "0.24", "7.6e−07", "0.30", "5.1e−10", "0.10", "0.05", "0.11", "0.02", "0.00", "0.99", "0.34", "2.8e−13"], ["ACO2", "0.18", "0.00", "0.11", "0.02", "−0.06", "0.17", "0.04", "0.41", "−0.03", "0.58", "−0.03", "0.58", "0.10", "0.05", "−0.04", "0.45", "0.24", "3.6e−07"], ["IDH1", "0.12", "0.01", "0.08", "0.11", "0.01", "0.77", "0.06", "0.21", "0.16", "0.00", "0.09", "0.08", "0.01", "0.88", "0.02", "0.63", "0.17", "0.00"], ["IDH2", "0.16", "0.00", "0.07", "0.13", "0.11", "0.03", "0.07", "0.14", "0.09", "0.08", "0.05", "0.27", "−0.03", "0.51", "0.04", "0.39", "0.25", "2.6e−07"], ["IDH3A", "0.16", "0.00", "−0.09", "0.06", "−0.04", "0.44", "0.07", "0.15", "0.09", "0.06", "0.04", "0.37", "−0.03", "0.58", "−0.01", "0.77", "0.24", "4.2e−07"], ["IDH3B", "−0.08", "0.12", "0.09", "0.06", "0.09", "0.07", "0.04", "0.48", "0.03", "0.60", "−0.05", "0.35", "0.06", "0.21", "0.04", "0.47", "0.24", "6e−07"], ["SUCLG1", "0.13", "0.01", "0.16", "0.00", "0.01", "0.86", "0.01", "0.81", "0.13", "0.01", "0.00", "0.90", "0.00", "0.99", "0.03", "0.50", "0.04", "0.41"], ["SUCLG2", "0.19", "9.3e−05", "0.01", "0.89", "−0.08", "0.12", "0.05", "0.27", "0.06", "0.22", "0.08", "0.12", "0.11", "0.02", "0.00", "0.90", "0.05", "0.28"], ["MDH2", "0.20", "4.4e−05", "0.00", "0.92", "−0.1", "0.05", "0.00", "0.96", "0.00", "0.97", "0.01", "0.79", "0.07", "0.17", "0.01", "0.87", "0.10", "0.04"], ["ME2", "0.27", "9.6e−09", "0.16", "0.00", "0.05", "0.33", "0.08", "0.09", "0.09", "0.07", "0.04", "0.45", "0.13", "0.01", "−0.03", "0.65", "0.12", "0.01"]], "row_count": 13, "column_count": 19, "numeric_cells": 203, "header_rows": 2, "locator": "section[8]/table-wrap[1]#cancers-12-01267-t002"}}, {"id": "asset:table:pmid:32429566:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:02b3e3c8c267d29c4ce12b15d1f9da6fa6f9befa364cede27fc273a85f8aeb53", "bytes": 7676, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#cancers-12-01267-t003", "version": null, "note": "Pearson correlation between the expression of CSC transcripts and the transcripts of the key enzymes involved in the ETC in patients’ data curated from TCGA. Red indicates significant positive, blue indicates negative correlations, and black indicates insignificant p-values of either positive or negative correlations.", "structure": {"pmcid": "PMC7281273", "section_index": 9, "section_title": "3.4. OXPHOS in Ovarian Cancer Stem Cells", "row_count": 51, "column_count": 19}, "table": {"label": "Table 3", "caption": "Pearson correlation between the expression of CSC transcripts and the transcripts of the key enzymes involved in the ETC in patients’ data curated from TCGA. Red indicates significant positive, blue indicates negative correlations, and black indicates insignificant p-values of either positive or negative correlations.", "rows": [["TCGA", ""], ["", "CD44", "", "CD24", "", "CD117", "", "CD133", "", "ALDH1A1", "", "SOX2", "", "4-Oct", "", "NANOG", "", "NOTCH1", ""], ["Complex I", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value"], ["NDUFA10", "0.04", "0.44", "0.02", "0.72", "−0.02", "0.72", "−0.03", "0.52", "0.09", "0.06", "−0.02", "0.62", "−0.03", "0.53", "0.00", "0.93", "0.10", "0.05"], ["NDUFA11", "−0.02", "0.62", "0.08", "0.10", "0.00", "0.93", "−0.05", "0.29", "−0.01", "0.86", "−0.02", "0.67", "−0.07", "0.16", "0.05", "0.30", "−0.15", "0.00"], ["NDUFAF4", "−0.12", "0.01", "0.23", "1.6e−06", "−0.06", "0.22", "−0.09", "0.05", "0.03", "0.54", "−0.02", "0.76", "0.00", "1.00", "0.05", "0.29", "−0.13", "0.01"], ["NDUFA2", "−0.13", "0.01", "−0.03", "0.48", "−0.19", "1e−04", "−0.11", "0.02", "−0.02", "0.66", "−0.02", "0.64", "−0.09", "0.06", "0.01", "0.83", "−0.29", "1.7e−09"], ["NDUFB7", "−0.12", "0.01", "−0.02", "0.67", "−0.15", "0.00", "−0.09", "0.06", "−0.05", "0.32", "−0.04", "0.40", "−0.07", "0.15", "0.03", "0.49", "−0.18", "0.00"], ["NDUFS1", "0.20", "2.8e−05", "0.16", "0.00", "0.14", "0.00", "0.14", "0.00", "0.17", "0.00", "0.02", "0.69", "0.07", "0.14", "0.03", "0.57", "0.39", "0.00"], ["NDUFS2", "0.18", "0.00", "0.13", "0.01", "0.15", "0.00", "0.13", "0.01", "0.06", "0.23", "0.09", "0.06", "0.15", "0.00", "0.16", "0.00", "0.36", "1.3e−14"], ["NDUFS3", "0.12", "0.01", "−0.05", "0.29", "−0.12", "0.01", "−0.02", "0.74", "0.00", "0.93", "0.04", "0.39", "0.04", "0.39", "0.02", "0.62", "−0.10", "0.05"], ["NDUFS7", "0.15", "0.00", "−0.02", "0.73", "−0.18", "0.00", "−0.08", "0.10", "−0.03", "0.49", "−0.01", "0.89", "−0.01", "0.86", "−0.02", "0.69", "−0.11", "0.02"], ["NDUFV1", "0.05", "0.33", "−0.02", "0.71", "−0.13", "0.01", "−0.01", "0.80", "−0.04", "0.43", "0.03", "0.51", "0.18", "0.00", "0.03", "0.61", "0.08", "0.11"], ["NDUFV2", "−0.02", "0.71", "0.05", "0.29", "−0.11", "0.02", "0.15", "0.00", "0.02", "0.65", "0.06", "0.18", "−1e−04", "1.00", "0.05", "0.35", "0.01", "0.88"], ["NDUFV3", "0.06", "0.24", "−0.01", "0.84", "−0.03", "0.56", "0.07", "0.14", "0.09", "0.07", "0.03", "0.52", "0.10", "0.03", "0.08", "0.10", "0.15", "0.00"], ["Complex II", ""], ["SDHA", "0.11", "0.03", "0.03", "0.52", "−0.04", "0.46", "0.05", "0.35", "0.03", "0.52", "0.11", "0.03", "0.06", "0.20", "0.04", "0.39", "0.16", "0.00"], ["SDHB", "0.18", "0.00", "0.09", "0.07", "−0.05", "0.28", "0.05", "0.29", "−0.02", "0.76", "−0.05", "0.29", "0.08", "0.10", "−0.03", "0.56", "0.03", "0.54"], ["SDHC", "0.16", "0.00", "0.11", "0.03", "0.10", "0.04", "0.07", "0.15", "0.21", "1.4e−05", "0.06", "0.23", "−0.0029", "0.95", "0.11", "0.03", "0.11", "0.02"], ["SDHD", "0.03", "0.59", "0.08", "0.09", "−0.12", "0.01", "0.02", "0.72", "0.00", "0.96", "0.02", "0.75", "0.04", "0.46", "−0.04", "0.43", "−0.03", "0.48"], ["Complex III", ""], ["UQCRB", "−0.12", "0.02", "−0.06", "0.19", "−0.20", "2.6e−05", "−0.08", "0.09", "−0.14", "0.00", "−0.06", "0.20", "−0.1", "0.04", "−0.04", "0.47", "−0.20", "2.1e−05"], ["UQCRC1", "0.03", "0.54", "0.08", "0.09", "0.00", "0.94", "0.06", "0.25", "0.08", "0.09", "0.04", "0.39", "0.06", "0.20", "0.13", "0.01", "0.17", "0.00"], ["UQCRC2", "0.21", "1.3e−05", "0.17", "0.00", "0.05", "0.31", "0.07", "0.17", "0.00", "0.92", "−0.06", "0.23", "0.15", "0.00", "0.04", "0.37", "0.07", "0.16"], ["UQCRH", "−0.04", "0.42", "−0.13", "0.01", "−0.13", "0.01", "−0.01", "0.82", "−0.01", "0.84", "0.00", "1.00", "−0.03", "0.58", "−0.08", "0.12", "−0.17", "0.00"], ["UQCRQ", "−0.05", "0.34", "−0.06", "0.20", "−0.17", "0.00", "−0.06", "0.19", "−0.03", "0.60", "−0.02", "0.70", "−0.01", "0.77", "−0.04", "0.41", "−0.31", "3.6e−11"], ["UQCR10", "0.04", "0.43", "0.15", "0.00", "−0.1", "0.04", "0.03", "0.50", "0.00", "0.97", "−0.02", "0.70", "0.06", "0.23", "−0.02", "0.66", "−0.11", "0.02"], ["UQCR11", "−0.03", "0.57", "−0.05", "0.32", "−0.21", "9.6e−06", "−0.10", "0.04", "−0.07", "0.18", "−0.03", "0.50", "−0.1", "0.04", "−0.03", "0.59", "−0.29", "8e−10"], ["CYCS", "0.09", "0.05", "0.07", "0.18", "−0.06", "0.20", "−0.04", "0.43", "0.09", "0.06", "−0.02", "0.73", "0.02", "0.64", "0.03", "0.60", "0.11", "0.03"], ["Complex IV", ""], ["COX4I1", "0.01", "0.81", "0.10", "0.05", "−0.15", "0.00", "0.03", "0.57", "−0.09", "0.07", "−0.06", "0.26", "0.03", "0.50", "−0.06", "0.21", "−0.19", "1e−04"], ["COX4I2", "−0.07", "0.18", "0.06", "0.22", "0.25", "2.2e−07", "0.01", "0.83", "0.17", "0.00", "−0.01", "0.82", "−0.08", "0.10", "0.16", "0.00", "0.15", "0.00"], ["COX5A", "0.00", "0.95", "−0.09", "0.08", "−0.19", "9.3e−05", "−0.04", "0.42", "0.00", "0.95", "−0.04", "0.43", "−0.04", "0.42", "−0.05", "0.31", "−0.13", "0.01"], ["COX5B", "−0.22", "6.6e−06", "0.10", "0.04", "−0.18", "0.00", "−0.07", "0.13", "−0.09", "0.08", "−0.02", "0.64", "−0.02", "0.68", "−0.04", "0.36", "−0.27", "1.7e−08"], ["COX6A1", "−0.1", "0.04", "0.03", "0.53", "−0.11", "0.03", "−0.06", "0.23", "0.07", "0.13", "0.01", "0.87", "−0.10", "0.04", "0.06", "0.19", "−0.12", "0.02"], ["COX6A2", "−0.13", "0.01", "0.09", "0.06", "0.20", "3.1e−05", "0.00", "0.92", "0.14", "0.00", "0.02", "0.69", "−0.07", "0.14", "0.24", "3.6e−07", "0.04", "0.39"], ["COX6B1", "−0.06", "0.21", "−0.03", "0.61", "−0.02", "0.73", "−0.06", "0.23", "0.07", "0.15", "−0.01", "0.87", "0.01", "0.85", "0.07", "0.15", "−0.19", "0.00"], ["COX6B2", "−0.04", "0.38", "−0.01", "0.77", "0.06", "0.20", "−0.03", "0.54", "0.00", "0.94", "−0.03", "0.48", "0.00", "0.96", "0.07", "0.15", "0.23", "2.6e−06"], ["COX6C", "−0.09", "0.05", "−0.12", "0.01", "−0.20", "5e−05", "−0.032", "0.51", "−0.13", "0.01", "−0.04", "0.39", "−0.12", "0.01", "−0.01", "0.91", "−0.12", "0.01"], ["COX7A1", "−0.02", "0.64", "−0.06", "0.24", "0.13", "0.01", "−0.03", "0.56", "0.08", "0.09", "−0.04", "0.38", "−0.06", "0.19", "0.02", "0.67", "0.00", "0.99"], ["COX7A2", "−0.08", "0.09", "0.09", "0.05", "−0.04", "0.40", "−0.09", "0.06", "0.02", "0.74", "0.00", "0.93", "−0.08", "0.09", "0.01", "0.87", "−0.19", "5.8e−05"], ["COX7B", "−0.02", "0.70", "−0.01", "0.78", "−0.19", "1e−04", "−0.07", "0.14", "0.01", "0.78", "0.00", "0.95", "−0.07", "0.15", "0.00", "0.98", "−0.27", "1.1e−08"], ["COX7C", "−0.21", "9.9e−06", "0.03", "0.55", "−0.08", "0.09", "−0.09", "0.08", "−0.10", "0.04", "−0.09", "0.06", "0.00", "0.96", "−0.01", "0.84", "−0.30", "2.8e−10"], ["Complex V", ""], ["ATP5C1", "0.03", "0.51", "0.08", "0.11", "−0.06", "0.24", "−0.06", "0.22", "−0.02", "0.62", "0.01", "0.87", "−0.05", "0.36", "−0.05", "0.28", "−0.07", "0.13"], ["ATP5D", "−0.02", "0.63", "−0.01", "0.91", "−0.22", "7.6e−06", "−0.11", "0.02", "−0.15", "0.00", "−0.06", "0.26", "0.00", "0.93", "−0.04", "0.38", "−0.18", "0.00"], ["ATP5E", "−0.14", "0.00", "0.00", "0.93", "−0.05", "0.33", "−0.03", "0.54", "0.03", "0.52", "0.06", "0.26", "−0.10", "0.04", "0.02", "0.76", "−0.19", "0.00"], ["ATP5G3", "0.07", "0.14", "−0.04", "0.36", "−0.16", "0.00", "−0.08", "0.08", "−0.01", "0.87", "−0.06", "0.23", "−0.05", "0.34", "−0.07", "0.17", "−0.13", "0.01"], ["ATP5J", "−0.03", "0.52", "−0.02", "0.65", "−0.10", "0.05", "−0.04", "0.44", "0.17", "0.00", "−0.01", "0.84", "0.01", "0.89", "0.00", "0.97", "−0.17", "0.00"], ["ATP5O", "−0.10", "0.04", "−0.02", "0.75", "−0.10", "0.03", "−0.06", "0.23", "−0.07", "0.14", "−0.07", "0.14", "0.06", "0.25", "0.04", "0.46", "−0.19", "0.00"], ["ATP5S", "0.02", "0.71", "0.00", "0.99", "0.08", "0.10", "0.10", "0.03", "0.14", "0.00", "−0.01", "0.78", "0.05", "0.32", "0.13", "0.01", "0.10", "0.04"]], "row_count": 51, "column_count": 19, "numeric_cells": 801, "header_rows": 3, "locator": "section[9]/table-wrap[1]#cancers-12-01267-t003"}}, {"id": "asset:table:pmid:32429566:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c09953c5c5be5e51d6f3c69469e1f975b6280fb5b29bbb34255f7d8c338a7ff0", "bytes": 2163, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#cancers-12-01267-t004", "version": null, "note": "Correlation between OCSC markers and lipid transporters and key enzymes in lipid metabolism in TCGA. Red indicates significant positive, and black indicates insignificant p-values of either positive or negative correlations.", "structure": {"pmcid": "PMC7281273", "section_index": 10, "section_title": "3.5. Correlation of OCSC Markers With Lipid Metabolism", "row_count": 12, "column_count": 19}, "table": {"label": "Table 4", "caption": "Correlation between OCSC markers and lipid transporters and key enzymes in lipid metabolism in TCGA. Red indicates significant positive, and black indicates insignificant p-values of either positive or negative correlations.", "rows": [["TCGA", "CD44", "", "CD24", "", "CD117", "", "CD133", "", "ALDH1A1", "", "SOX2", "", "4-Oct", "", "NANOG", "", "NOTCH1", ""], ["", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value"], ["FABP4", "0.04", "0.43", "−0.04", "0.44", "0.05", "0.28", "−0.07", "0.13", "0.05", "0.33", "−0.04", "0.43", "0.00", "0.87", "−0.06", "0.21", "0.07", "0.13"], ["CD36", "0.17", "0.00", "−0.02", "0.63", "0.11", "0.02", "−0.07", "0.14", "0.09", "0.07", "0.03", "0.51", "−0.03", "0.55", "0.00", "0.90", "0.24", "4e−07"], ["ACLY", "0.21", "9e−06", "0.13", "0.01", "0.37", "3.1e−15", "0.21", "1.8e−05", "0.15", "0.00", "0.04", "0.43", "0.01", "0.85", "0.12", "0.02", "0.51", "0.00"], ["ACACA", "0.16", "0.00", "0.20", "3.1e−05", "0.19", "0.00", "0.22", "4.5e−06", "0.10", "0.03", "0.01", "0.79", "0.08", "0.11", "0.02", "0.73", "0.32", "6.3e−12"], ["ACACB", "0.10", "0.04", "0.00", "0.99", "0.27", "1.7e−08", "0.11", "0.02", "0.13", "0.01", "0.03", "0.58", "0.10", "0.04", "0.12", "0.02", "0.40", "0.00"], ["CPT1A", "0.12", "0.01", "0.03", "0.56", "0.11", "0.02", "0.16", "0.00", "0.09", "0.07", "0.06", "0.20", "0.09", "0.07", "0.00", "0.89", "0.35", "7.1e−14"], ["CPT1B", "0.16", "0.00", "−0.07", "0.15", "−0.05", "0.30", "−0.02", "0.64", "0.00", "0.93", "0.12", "0.02", "0.13", "0.01", "0.08", "0.11", "0.17", "3e−04"], ["CPT2", "0.19", "7.7e−05", "0.03", "0.57", "0.08", "0.08", "0.18", "0.00", "0.18", "0.00", "0.09", "0.06", "0.06", "0.20", "0.09", "0.07", "0.29", "7.1e−10"], ["FASN", "0.08", "0.08", "0.06", "0.25", "0.10", "0.03", "0.05", "0.31", "0.05", "0.28", "0.00", "0.85", "−0.02", "0.66", "0.02", "0.67", "0.42", "0.00"], ["SCD1", "0.27", "1.3e−08", "0.06", "0.20", "0.11", "0.02", "0.08", "0.10", "0.08", "0.12", "0.11", "0.03", "−0.05", "0.28", "−0.02", "0.67", "0.27", "1.5e−08"]], "row_count": 12, "column_count": 19, "numeric_cells": 186, "header_rows": 2, "locator": "section[10]/table-wrap[1]#cancers-12-01267-t004"}}, {"id": "asset:table:pmid:32429566:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:31b381770795ed5f0ac12b44026fa7062da3fe04a91f903c2486f7145e0aa874", "bytes": 2233, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#cancers-12-01267-t005", "version": null, "note": "Correlation between OCSC markers and glutamate transporters and key enzymes in glutamate/glutamine metabolism in TCGA. Red indicates significant positive and black indicates insignificant p-values of either positive or negative correlations.", "structure": {"pmcid": "PMC7281273", "section_index": 11, "section_title": "3.6. Glutamine/Glutamate Metabolism in OCSCs", "row_count": 12, "column_count": 19}, "table": {"label": "Table 5", "caption": "Correlation between OCSC markers and glutamate transporters and key enzymes in glutamate/glutamine metabolism in TCGA. Red indicates significant positive and black indicates insignificant p-values of either positive or negative correlations.", "rows": [["TCGA", "CD44", "", "CD24", "", "CD117", "", "CD133", "", "ALDH1A1", "", "SOX2", "", "4-Oct", "", "NANOG", "", "NOTCH1", ""], ["", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value"], ["SLC1A1", "0.32", "1.2e−11", "0.10", "0.05", "0.04", "0.39", "0.20", "3.9e−05", "0.12", "0.01", "0.15", "0.00", "0.18", "0.00", "−0.04", "0.40", "0.09", "0.06"], ["SLC1A2", "0.16", "0.00", "0.00", "0.93", "0.25", "1e−07", "0.12", "0.01", "0.22", "4.1e−06", "0.05", "0.31", "0.04", "0.44", "0.07", "0.13", "0.14", "0.00"], ["SLC1A3", "0.20", "4.6e−05", "0.08", "0.12", "0.09", "0.08", "0.18", "0.00", "−0.04", "0.47", "0.08", "0.11", "0.20", "4.8e−05", "−0.01", "0.82", "0.15", "0.00"], ["SLC1A4", "0.27", "1.5e−08", "−0.03", "0.60", "0.27", "1.8e−08", "0.13", "0.01", "0.25", "2.3e−07", "0.11", "0.02", "0.00", "0.99", "0.09", "0.06", "0.36", "1.4e−14"], ["SLC1A5", "0.24", "3.7e−07", "−0.08", "0.10", "0.06", "0.21", "0.03", "0.56", "0.05", "0.35", "0.15", "0.00", "0.03", "0.50", "−0.03", "0.58", "0.22", "7.4e−06"], ["SLC1A6", "−0.02", "0.64", "0.02", "0.76", "0.03", "0.53", "0.02", "0.69", "0.00", "0.96", "0.01", "0.78", "−0.04", "0.38", "0.06", "0.21", "0.04", "0.40"], ["SLC1A7", "0.09", "0.08", "−0.06", "0.21", "0.43", "0.00", "0.25", "2.4e−07", "0.16", "0.00", "−0.05", "0.35", "−0.03", "0.50", "−0.04", "0.47", "0.33", "2e−12"], ["GLS", "0.15", "0.00", "−0.01", "0.86", "0.11", "0.02", "−0.01", "0.86", "0.18", "0.00", "0.03", "0.49", "0.05", "0.30", "0.13", "0.01", "0.36", "2.8e−14"], ["GLUD1", "0.10", "0.03", "0.02", "0.73", "0.11", "0.03", "0.06", "0.20", "0.11", "0.02", "−0.02", "0.68", "0.14", "0.00", "0.05", "0.35", "0.25", "2.2e−07"], ["GLUD2", "0.19", "7.8e−05", "0.04", "0.73", "0.25", "2.6e−07", "0.05", "0.31", "0.26", "4.8e−08", "0.09", "0.08", "0.15", "0.00", "0.31", "9.3e−11", "0.27", "1.3e−08"]], "row_count": 12, "column_count": 19, "numeric_cells": 185, "header_rows": 2, "locator": "section[11]/table-wrap[1]#cancers-12-01267-t005"}}], "gaps": ["asset:data:geo:GSE28799 not downloaded", "asset:data:geo:GSE28799 licence not read", "asset:data:geo:GSE64999 not downloaded", "asset:data:geo:GSE64999 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson Correlation"}}, {"id": "method-2", "family": null, "specific": null, "label": "multiple t-test with Holm–Sidak method", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The differential expression of the OCSCs markers and the enzymes involved in the metabolic pathways in OCSCs and their parental cells was analyzed by the multiple t-test with Holm–Sidak method, and each gene was analyzed individually between the two groups, without assuming a consistent SD with p ≤ 0.05."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["pearson_r"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pearson."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE28799", "GSE64999"], "resolved_accessions": ["GSE28799", "GSE64999"], "statements": ["Gene expression profiles of two studies of OCSC GSE28799 [41] and GSE64999 [42] with platform information of GPL570 and GPL17077, respectively, were extracted from Gene Expression Omnibus (GEO). Both included ovarian cancer spheroids and their parental cells. GSE28799 included OVCAR3-derived spheroids and their parental OVCAR3 in triplicates."], "basis": "The paper names GSE28799, GSE64999 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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