DOI: 10.7910/dvn/oxwtex
title: Transcriptome changes associated with elongation of bovine conceptuses I: differentially expressed transcripts in the conceptus on day 17 after insemination_JDS23398

description: The dataset provided contains supplemental files that are part of the article entitled: "Transcriptome changes associated with elongation of bovine conceptuses I: differentially expressed transcripts in the conceptus on day 17 after insemination"

Supplemental Table S1. Complete list of transcripts evaluated using the Affymetrix Gene Chip Bovine Array. Probe ID = Affymetrix denomination for each probe; gene symbol = recovered from the Ensemble database based on probeID; EntrezGene = reference number for Bos Taurus recovered from NCBI database; Log2FC = Log2 fold-change; adj.P = P-value adjusted for false discovery rate; DET = dummy indicator identifying whether each transcript was differentially expressed (|Log2FC| ≥ 0.58; adj. P ≤ 0.05) for the referred comparison (0 = not differentially expressed; 1 = upregulated; -1 = downregulated). Additionally, it contains a list of DET for each comparison whenever one of the filters (Log2FC or adj.P-value) are removed.

Supplemental Table S2. Complete list of diseases and biofunctions from the Ingenuity Pathway Analyses platform. The smaller conceptus length category within each comparison was considered the reference group. OP = P-value of overlap calculated using a right-tail Fisher’s exact test; ZS = Z-score for prediction of increased or decreased activation of biological functions based on the fold change of DET offered to the software; N/A = ZS not calculated by Ingenuity Pathway Analyses. Predicted activation state was increased if ZS ≥ 2.00 or decreased if ZS ≤ -2.00.

Supplemental Table S3. Complete list of canonical pathways from the Ingenuity Pathway Analyses platform. For comparisons involving size, the smaller conceptus length category within each comparison was considered the reference group. For the comparison involving sex, female conceptuses were considered as the reference group. 
Ratio = proportion of the total number of molecules described for each pathway that were identified as DET in the study database; ZS = Z-score for prediction of increased or decreased activation of biological functions based on the fold change of DET offered to the software; N/A = ZS not calculated by Ingenuity Pathway Analyses.

Supplemental Table S4. Complete list of upstream regulators from the Ingenuity Pathway Analyses platform. Expression log ratio = log fold-change for DET in the study database that were also predicted to be upstream regulators by Ingenuity Pathway Analyses; OP = P-value of overlap calculated using a right-tail Fisher’s exact test; ZS = Z-score for prediction of increased or decreased activation of biological functions based on the fold change of DET offered to the software; N/A = ZS not calculated by Ingenuity Pathway Analyses. Predicted activation state was activated if ZS ≥ 2.00 or inhibited if ZS ≤ -2.00.

Supplemental Table S5. Complete list of DET associated with the average maternal circulation of progesterone (4.047 ng/ml, 2.613 to 6.537 ng/ml) from d 0 to 17 of gestation, that were also differently expressed in at least one of the length comparisons. It contains the list of the 165 unique and with known annotation DET, and linear regression features such as: R2, intercept, slope and the P-value adjusted for FDR. The associated DET are sorted based on the number of canonical pathways that it was associated in each respective length comparison (LvsS, LvsM and MvsS). Additionally, it contains the information if the 165 transcripts associated with progesterone, were upregulated (1) or downregulated (-1), for the each of the three length comparisons.

Supplemental Table S6. Complete list of canonical pathways linked with DET correlated with progesterone. The association of the DET and the canonical pathways is stratified by each length comparison. The -log(P-value) and the ZS, refers to the length association with the respective canonical pathway.

Supplemental Figure S1. Regulator effects predicted for the comparison between large (L; 21.9 ± 2.5 cm; 18.0 to 26.4 cm) and medium conceptuses (M; 13.4 ± 1.6 cm; 10.5 to 16.0 cm) on d 17 after AI. Dashed and solid lines represent direct and indirect effects between molecules and transcripts, respectively. Orange = predicted activation; blue = predicted inhibition; gray = no pattern of activation or inhibition available; yellow = predicted activity in the dataset was contrary to that described in the IPA library. Upregulated transcripts are presented in red (i.e., darker red indicates greater absolute log2 fold change).