1. Network analyses of differentially expressed proteins in amniotic fluid supernatant associated with abnormal human karyotypes 
Tzu-Hao Wang, M.D., Ph.D., An-Shine Chao, M.D., Jen-Kun Chen, Ph.D., Angel Chao, M.D., Ph.D., Yao-Lung Chang, M.D., Po-Jen Cheng, M.D., Shuenn-Dyh Chang, M.D., Hsin-Shih Wang, M.D., Ph.D. 
Fertility and Sterility 
Volume 92, Issue 1, Pages (July 2009)
DOI: /j.fertnstert
Copyright © 2009 American Society for Reproductive Medicine Terms and Conditions

2. Figure 1
Flow chart of study design. ProteomeLab PF 2D was used as a screening tool for detecting differentially expressed proteins among three AFS groups: in normal, trisomy-18, and trisomy-21 gestations. Subsequently, candidate proteins were verified by measuring their levels in a larger testing set of AFS samples (34 normal, 17 trisomy 18, and 19 trisomy 21) using Western blot analysis or ELISA. SDS-PAGE = sodium dodecyl sulfate polyacrylamide gel electrophoresis; MALDI-TOF MS = matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
Fertility and Sterility  , DOI: ( /j.fertnstert )
Copyright © 2009 American Society for Reproductive Medicine Terms and Conditions

3. Figure 2
Two-dimensional visualization of protein profiles and comparisons of protein amounts in the matched fractions of the second dimension. (A) Comparisons between normal and trisomy 18. Fractions of every 0.3 pH units from pH 8.5 to 4 were collected and are displayed in the x-axis. The second dimension elution time from 2 to 27 minutes is indicated in the y-axis (left panel). Quantitative comparisons of normalized protein amounts at matched fractions collected in the second dimension are shown (right panel). (B) Comparisons between normal and trisomy 21.
Fertility and Sterility  , DOI: ( /j.fertnstert )
Copyright © 2009 American Society for Reproductive Medicine Terms and Conditions

4. Figure 3
Normalization of densitometry levels of each specific protein identified by Western blot analysis with the total protein input of each sample. After proteins in sodium dodecyl sulfate polyacrylamide gel electrophoresis were transferred, resulting nitrocellulose membranes were stained with Ponceau S dye and scanned. During Western blot analysis, protein bands detected by a specific antibody (anti-placental protein 14 in this example) were also scanned. Densitometry quantifications were performed using UN-SCAN-IT software. Densitometry level of each sample, either in Ponceau S staining or in Western blot analysis, was represented as a percentage of those in the whole membrane that was set as 100%. Therefore, after normalization, results derived from different nitrocellulose membranes can be analyzed for statistical significance.
Fertility and Sterility  , DOI: ( /j.fertnstert )
Copyright © 2009 American Society for Reproductive Medicine Terms and Conditions

5. Figure 4
Biologic network analyses of differentially expressed proteins using MetaCore mapping tools. (A) Using the MetaCore program, three differentially expressed proteins in trisomy-18 amniotic fluid (as shown as solid circles; green arrows indicate decreased levels in trisomy 18) were found to interact with proteins in this network. Some proteins are shown as gene symbols: APOA1 = apolipoprotein A1; SERPINA3 = α1 antitrypsin. The related biologic processes in this network are listed in Table 2. (B) Four differentially expressed proteins in trisomy-21 amniotic fluid (as shown as solid circles; red arrows indicate increased protein levels, and green arrows indicate decreased levels in trisomy 21) were found to interact with proteins in this network. Nodes represent proteins; lines between the nodes indicate direct protein–protein interaction. Some proteins are shown as alias, such as transthyretin = prealbumin. The related biologic processes in this network are listed in Table 3.
Fertility and Sterility  , DOI: ( /j.fertnstert )
Copyright © 2009 American Society for Reproductive Medicine Terms and Conditions