This file contains the canonical pathway enrichment output from Ingenuity Pathway Analysis (IPA), performed on the list of differentially expressed genes identified at the 3-hour post-weaning time point. Columns include pathway name, -log(Benjamini-Hochberg p-value), enrichment ratio, activation z-score, and the list of associated genes ("Molecules") mapped to each pathway.

Genes tested by RT-PCR are highlighted in bold and underlined.*(number of genes regulated in the same direction).†top transcription factors for each analysis as assessed by GePS.

List of top 20 toxicity pathways induced by TWEAK in C2C12 cells. Ingenuity pathway analysis was used to generate the toxicity pathways involved by differentially expressed genes by TWEAK with p-values≤0.05 and ≥1.2-fold. Negative logarithmic p-values in the table are Fisher's exact test p-value which determines the probability of the association between the genes in the data set and the canonical pathway. Ratio was calculated by the genes in the data set involved in a particular toxicity pathway divided by total number of genes involved in that pathway.

The table shows results for 439 probes representing 391 genes concordant for differential expression (adjusted P-value 2-fold change) when comparing active VL cases with healthy controls across experiments 1 and 2, and for 221 probes representing 210 genes concordant for differential expression (adjusted P = value

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).

Ingenuity pathway analysis (IPA) in The Cancer Genome Atlas (TCGA) union of RNA seq and Agilent data. Top canonical pathways detected by IPA using the union of differentially expressed genes in Agilent and RNA-Seq expression platforms in TCGA. Four columns correspond to Ingenuity canonical pathway names, −log(p value), percentage of genes detected in this pathway, and molecules in this pathway. (XLS 15 kb)

The Cancer Genome Atlas (TCGA) Ingenuity pathway analysis (IPA) upstream regulators. Table S1., Table S2. Top upstream regulators detected by IPA using the union of differentially expressed genes in Agilent and RNA-Seq expression platforms in TCGA. Table S2. Top upstream regulators detected by IPA using the differentially expressed gene list from Agilent expression array. Four columns correspond to Ingenuity canonical pathway names, −log(p value), percentage of genes detected in this pathway, and molecules in this pathway. Table S3. Top upstream regulators detected by IPA using the differentially expressed gene list from RNA-Seq expression array. Four columns correspond to Ingenuity canonical pathway names, −log(p value), percentage of genes detected in this pathway, and molecules in this pathway. (XLS 177 kb)

Note: the “Ratio” was calculated from dividing the number of metabolites that map to the canonical pathway by the total number of molecules that map to the pathway; the “P-value” was calculated from Fisher’s exact test; the “Score” indicates the association between the molecules and the network. See the Materials and Methods section for details.

aThe top 25 of 79 enriched functional categories are shown.bBenjamini-Hochberg adjusted p-values were back calculated from −log values given by IPA by using those values as exponents to −10 (i.e. −100.05).

Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) Ingenuity pathway analysis (IPA) upstream regulators. Top canonical upstream regulators detected by IPA using the list of differentially expressed genes in METABRIC. Four columns correspond to the Ingenuity canonical pathway names, −log(p value), percentage of genes detected in this pathway, and molecules in this pathway. (XLSX 35 kb)

The most significant canonical pathways and corresponding -values calculated by Ingenuity Pathway Analysis.

The Functional Analysis of a Network identified biological functions and/or diseases that were most significant to the molecules in the network using a right-tailed Fisher's exact test.Canonical Pathway Analysis identified pathways from the IPA library that were most significant to the data set.Significance of the association was measured in two ways: (1) as the ratio of the number of molecules from the focus gene set that map to the pathway to the total number of molecules that map to the canonical pathway and (2) using Fisher's exact test.**Transcription factor analysis is based on prior knowledge of expected effects between transcription factors and their target genes stored in the IPA library.The overlap p-value measures whether there is a statistically significant overlap between the dataset genes and the genes regulated by a transcription factor using Fisher's Exact Test.

Note: GABA: γ-Aminobutyric acid; the “Ratio” was calculated from dividing the number of metabolites that map to the canonical pathway by the total number of molecules that map to the pathway; the “P-value” was calculated from Fisher’s exact test. See the Materials and Methods section for details.

Analysis of The Cancer Genome Atlas (TCGA) data showing canonical Wnt pathways genes expressed in BCL9-high versus BCL9-low tumors. TCGA breast cancer samples with BCL9 levels above the range defined by normal samples were labeled upregulated in cancer (414 samples). The significant differentially expressed genes from TCGA analysis of BCL9-high versus BCL9-low tumors were analyzed in Ingenuity Pathway Analysis (IPA) and the canonical pathways with a p value ≤0.05 were obtained. (XLS 124 kb)

Significant results from Ingenuity Pathway Analysis -- Canonical Pathways. IPA results from the canonical pathways analysis for each combination of platform and aligner. Table lists pathway names, enrichment p-values, z-scores, and the list of DEGs for each pathway. (XLSX 35Â kb)

The top 6 canonical pathways (based on p value) generated by Ingenuity Pathway Analysis based on differentially expressed proteins in breast muscle obtained from broiler breeder males.

Evaluation of intestinal response to zinc restriction in pigs. Supplementary table 1 shows the growth performance of pigs in different treatment groups. Supplementary tables 2 and 3 show the differentially expressed genes (DEGs) in ZnR compared with Zn100 and Zn50 respectively. Supplementary tables 4-11 show the panther analysis of the DEGs. Supplementary figure 1 shows top three upregulated and downregulated canonical pathways through IPA analysis of differentially expressed genes in Zn100 compared with Zn50. Z-score >2 or

Significantly altered canonical pathways were obtained from metabolomics datasets using IPA and top four pathways are presented here along with corresponding p-value (-log) and molecules involved.

The top ranked Ingenuity canonical pathways resulting from differentially upregulated gene expression analysis (FC≥1.5 and p≤0.005) of the respective co-cultures were compared with each other. Calculation of significance was done by Fisher's exact test right-tailed. Canonical pathways exhibiting significant changes in at least three out of the four co-cultures are depicted. Numbers represent—log(p-value).Ingenuity Canonical Pathway Analysis.

The 480 differentially expressed genes targeted by miRNAs between SLKK and SLK cells were used as input for the Ingenuity pathway analysis (IPA). Here, we highlighted 4 of the top 10 enriched pathways that are relevant to KSHV pathogenesis. Columns identify the pathway name, its associated P-value, the ratio between dysregulated genes and genes in the pathway, which dysregulated target gene and miRNA are involved. Genes or miRNAs in bold and normal font were found up-regulated and down-regulated, respectively, by chronic KSHV infection.Canonical pathways affected by differentially expressed miRNA-mRNA pairs.