Table 4 Functional annotation of differentially expressed genes by Ingenuity Pathway Analysis (IPA). To investigate possible interactions of the differentially expressed RNAs, the datasets including the 663 upregulated RNAs (A, B, and C) and the 44 downregulated RNAs (D and E) in blastocysts cultured in biphasic (5%-2%) O2 concentration compared with monophasic (5%) O2 concentration were imported in the IPA Tool to identify the top signaling pathways, functions and interactions. A general overview of the pathways linked to embryo and fetal development are presented in the table with the number and the names of transcripts from the datasets that map to each pathway. For A, B, D and E, the right-tailed Fisher's exact test was used by IPA to determine whether the biological attribute was significantly enriched in the dataset (p ≤ 0.05 was considered significant). For C, the two highest consistency scores are presented. The consistency score is an indicator used to describe the causal consistency of the upstream regulatory factor in the network, the dataset and dense connection metric between disease and function.
A | Top molecular and cellular functions | P value range | # Transcripts | Transcript names |
|---|---|---|---|---|
RNA post-transcriptional modification | 8.43 × 10–3–2.73 × 10–4 | 16 | ADARB1, ATXN3, CTDP1, DDX52, GEMIN2, INTS8, INTS9, PELP1, PPARGC1A, RBPMS, SF3B6, SNRNP27, SRSF5, SYF2, THOC1, TRNT1 | |
Cellular assembly and organization | 1.50 × 10–2–3.32 × 10–4 | 25 | ADARB1, ATXN3, AURKC, BNIP3L, CCNB2, CTSV, DDX19B, DGUOK, DST, EHBP1, GNA12, IFT20, IL6, KIF22, KIF2C, LAMTOR1, MMS22L, NDC80, NUBPL, NUF2, PPARGC1A, PRKAA1, SMC6, SUCO, VDAC3 | |
DNA replication, recombination and repair | 1.08 × 10–2–3.32 × 10–4 | 26 | ADARB1, ATXN3, AURKC, CCNB2, COPS8, CTC1, DGUOK, IL6, KIF22, KIF2C, MMS22L, NDC80, NUF2, OARD1, OTUD6B, POLB, POLD1, RAD54B, RBBP5, RFC5, RRM1, SHLD1, SMC6, THOC1, TIGAR, ZBTB1 | |
Cell cycle | 1.77 × 10–2–6.91 × 10–4 | 22 | AJUBA, AURKC, BRAP, CCNB2, CDK19, CHKA, CTCF, EP400, GNA12, IL6, KIF15, KIF22, KIF2C, NDC80, NUF2, POLD1, PPP2CA, PRKAA1, RRM1, SMC6, TAF12, ZBTB1 | |
Cell death and survival | 1.49 × 10–2–6.91 × 10–4 | 26 | AKIP1, ATXN3, BAK1, BNIP3L, CHKA, CTH, DAPK1, EMC4, EP400, IL6, KIF15, MAP2K4, MINPP1, MMS22L, NDC80, NUF2, PPARGC1A, PP2CA, PRKAA1, RIPK1, SHLD1, SMC6, STK3, TFB1M, THOC1, TM2D1 |
Top physiological system development and function | P value range | # Transcripts | Transcript names | |
|---|---|---|---|---|
Organismal functions | 1.08 × 10–2–3.32 × 10–4 | 7 | CTCF, DGUOK, IL6, MAP2K4, POMT2, PPARGC1A, PRKAA1 | |
Digestive system development and function | 1.12 × 10–2–3.48 × 10–4 | 10 | ARV1, CTSV, DGUOK, IL6, MAP2K4, mir-597, POLB, POLD1, PPARGC1A, STK3 | |
Hepatic system development and function | 1.12 × 10–2–3.48 × 10–4 | 10 | ARV1, DGUOK, IGF2R, IL6, MAP2K4, mir-597, POLB, POLD1, PPARGC1A, STK3 | |
Organ development | 1.27 × 10–2–3.48 × 10–4 | 11 | ARV1, CTSV, DGUOK, IL6, MALT1, mir-597, POLB, POLD1, PPARGC1A, PRKAA1, STK3 | |
Embryonic development | 1.26 × 10–2–3.14 × 10–3 | 11 | CTCF, IL6, KIF22, MALT1, MAP2K4, POLD1, POMT2, PPARGC1A, SNAP23, TEFM, THOC1 |
B | Diseases or functions annotation | p value | # Transcripts | Transcripts in "Embryonic Development" |
|---|---|---|---|---|
Lack of embryoblast | 3.14E−03 | 2 | CTCF,THOC1 | |
Angiogenesis of cerebellum | 1.08E−02 | 1 | IL6 | |
Differentiation of Th22 cells | 1.08E−02 | 1 | IL6 | |
Development of anterior tibial muscle | 1.08E−02 | 1 | PPARGC1A | |
Cellularity of mesenteric lymph node | 1.08E−02 | 1 | MALT1 | |
Cellularity of cervical lymph node | 1.08E−02 | 1 | MALT1 | |
Death of embryo | 1.26E−02 | 6 | KIF22,MAP2K4,POLD1,POMT2,SNAP23,TEFM |
C | Disease and functions | Consistency Scores | # Transcripts | ID Regulator |
|---|---|---|---|---|
Morbidity or mortality | 2.236 | 5 | mi-R-16-5p (and other miRNAs we/seed AGCAGCA) | |
Organismal death | − 3.402 | 7 | CEBPB |
D | Top molecular and cellular functions | P value range | # Transcripts | Transcript names |
|---|---|---|---|---|
Cellular movement | 3.92 × 10–2–2.18 × 10–4 | 3 | AGER, NEO1, SLC41A2 | |
Cell death and survival | 3.65 × 10–2–9.06 × 10–4 | 9 | AGER, AMBRA1, BTBD10, CABLES1, FLCN, LTBP1, NEO1, NUP160, SLC41A2 | |
Cell-to-cell signaling and interaction | 3.57 × 10–2–9.06 × 10–4 | 4 | AGER, AMBRA1, LTBP1, NEO1 | |
Cellular assembly and organization | 3.04 × 10–2–1.81 × 10–3 | 5 | AGER, FLCN, KLHL15, NEO1, NUP160 | |
Cellular compromise | 8.13 × 10–3–1.81 × 10–3 | 1 | AGER |
Top physiological system development and function | ||||
|---|---|---|---|---|
Skeletal and muscular system development and function | 4.96 × 10–2–2.18 × 10–4 | 5 | AGER, KLF11, LTBP1, NEO1, SLC41A2 | |
Cardiovascular system development and function | 4.78 × 10–2–9.06 × 10–4 | 4 | AGER, KLF11, LTBP1, SLC41A2 | |
Nervous system development and function | 3.74 × 10–29.06 × 10–4 | 3 | AGER, KLHL15, NEO1 | |
Organismal development | 4.96 × 10–2–.06 × 10–4 | 7 | AGER, CABLES1, FLCN, KLF11, LTBP1, NEO1, SLC41A2 | |
Tissue morphology | 4.44 × 10–2–9.06 × 10–4 | 2 | AGER, LTBP1 |
E | Cell death and survival | P value | # Transcripts | Transcript names |
|---|---|---|---|---|
Apoptosis of embryonic stem cells | 3.57E−02 | 1 | FLCN | |
Organismal development | P value | # Transcripts | Transcript names | |
Differentiation of embryonic stem cells | 6.68E−03 | 2 | AGER,FLCN |
