This document discusses analyzing cell cycle microarray data. It mentions that microarrays allow measuring RNA levels of all genes at once using two technologies: mechanical spotting of cDNAs/ESTs/oligomer probes or photolithography using Affymetrix chips. The document discusses normalizing the data and examples of real-world cell cycle expression studies that analyzed synchronized cell cultures over time courses using microarrays and identified periodically expressed genes through various computational methods like Fourier analysis, pattern matching, and statistical tests.

1. Cell-cycle microarray analysis Lars Juhl Jensen EMBL Heidelberg

2. microarrays 101

3. RNA levels

4. all genes at once

6. two technologies

7. mechanical spotting

8. cDNAs

9. ESTs

10. oligomer probes

11. photolithography

12. Affymetrix

13. two types of data

14. one-channel

15. two-channel

16. normalization

17. noise vs. bias

19. real-world example

20. Downloaded SMD data After intensity normalization Spatial bias estimate After spatial normalization

21. cell-cycle expression

22. cell cultures

24. synchronization

25. isolate mRNA

26. microarrays

28. time courses

30. expression profiles

32. Cho et al.

34. visual inspection

35. Spellman et al.

37. Fourier score

38. Zhao et al.

40. single-pulse model

41. Johansson et al.

43. partial least squares

44. Langmead et al.

48. rhythmic analysis

49. Wichert et al.

51. Fisher’s G-statistic

52. Luan et al.

53. Luan et al.

55. cubic-splines model

56. Lu et al.

58. periodic-normal mixture

59. de Lichtenberg et al.

61. dual permutation test

62. Willbrand et al.

64. up-down patterns

65. Ahdesmäki et al.

67. Fisher’s G-statistic

68. Chen

70. Fisher’s G-statistic

71. Qiu et al.

74. resynchronization

75. Glynn et al.

77. Lomb-Scargle periodogram

78. Andersson et al.

80. Bayesian detector

81. Ahnert et al.

83. low entropy patterns

84. Xu et al.

86. partial energy ratio

87. Lu et al.

90. homology transfer

91. Liew et al.

93. Fisher’s G-statistic

94. Morton et al.

96. cyclohedron test

97. Rowicka et al.

99. correlation to known genes

100. things to consider

101. change

102. periodicity

103. shape

104. loss of synchrony

105. stress response

106. uneven sampling

107. missing data points

108. multiple experiments

109. one (ranked) list