WormBase Tree Display for Expression_cluster: WBPaper00026952:class_F

WBPaper00026952:class_F Description: Class F gene expression showed no change in lin-14(lf) in L1, down regulation in lin-4(lf) in L2.
  Species: Caenorhabditis elegans
  Algorithm: Raw data from each experiment were downloaded from the Stanford Microarray Database into Excel files and processed as follows: (i) sort by Spot Flag and discard any rows where the Spot Flag value was nonzero, indicating a bad PCR; (ii) sort by Failed and discard any rows where the Failed value was nonzero, indicating abnormal hybridization; (iii) import into a common file for each type of experiment (i.e., lin-14 or lin-4) the columns from each raw experimental file [RAT2(R/G), which shows a log base 2 transformed ratio of normalized red/green signal for each spot; name of spot (Wormbase designation); chromosome location and description (www.wormbase.org)]; (iv) calculate an average RAT2(R/G) based on the 2 or 3 values (avg; any rows which had only one good experimental value were discarded); (v) calculate a standard deviation (stdev) for the average value; (vi) calculate a t value for each spot by using the formula t = avg*[sqrt(n - 1)]/stdev, where n is the number of experiments for which good data exist, sqrt is square root, and stdev is standard deviation; (vii) sort by absolute t value and discard any rows with a t value below 4.303 (below 95% confidence interval for three experiments) or below 12.706 (below 95% confidence interval for two experiments); (viii) sort by absolute average value and discard any rows with average values below 1.0 (less than twofold change compared to control).
  Reference: WBPaper00026952
  Microarray_results: SMD_0ZK637.13
    SMD_C04F5.7
    SMD_C06G8.3
    SMD_C10E2.6
    SMD_C11H1.2
    SMD_C14E2.3
    SMD_C15C8.3
    SMD_C16C10.5
    SMD_C17H12.1
    SMD_C25F9.1
    SMD_C31B8.8
    SMD_C32F10.8
    SMD_C32H11.1
    SMD_C36A4.9
    SMD_C39D10.4
    SMD_C46F9.4
    SMD_C50F4.1
    SMD_C55A6.4
    SMD_C55A6.7
    SMD_D1005.1
    SMD_D1086.3
    SMD_EGAP4.1
    SMD_F01F1.12
    SMD_F01G10.3
    SMD_F07C4.6
    SMD_F08F3.3
    SMD_F09G8.4
    SMD_F13H8.5
    SMD_F14F7.1
    SMD_F16H6.1
    SMD_F19C7.7
    SMD_F20H11.3
    SMD_F21D5.3
    SMD_F22B8.6
    SMD_F22B8.7
    SMD_F22F7.1
    SMD_F23F12.1
    SMD_F23F12.10
    SMD_F23F12.3
    SMD_F25B4.1
    SMD_F32B5.1
    SMD_F32G8.4
    SMD_F32H5.3
    SMD_F38E11.3
    SMD_F40F4.3
    SMD_F40H3.2
    SMD_F41H10.4
    SMD_F42G2.5
    SMD_F42G8.7
    SMD_F44E7.4
    SMD_F44G3.10
    SMD_F46C5.1
    SMD_F46H5.3
    SMD_F48E3.2
    SMD_F54H5.3
    SMD_F55C9.2
    SMD_F56B3.1
    SMD_F57A10.3
    SMD_F57B1.4
    SMD_F58B4.1
    SMD_H20E11.2
    SMD_K01A2.2
    SMD_K04G2.7
    SMD_K04H4.5
    SMD_K07C6.3
    SMD_K08E7.9
    SMD_K08F4.5
    SMD_K10B3.8
    SMD_K10H10.2
    SMD_K12G11.3
    SMD_R07B1.10
    SMD_R08E5.3
    SMD_R09B5.6
    SMD_R09D1.8
    SMD_T01D3.6
    SMD_T06E4.6
    SMD_T08B2.9
    SMD_T12B5.13
    SMD_T13C2.1
    SMD_T19C9.8
    SMD_T19D7.1
    SMD_T21C9.8
    SMD_T22G5.6
    SMD_T25B9.1
    SMD_T25E12.10
    SMD_T28A11.12
    SMD_W05E7.1
    SMD_W07B8.4
    SMD_W08A12.1
    SMD_Y102A5C.20
    SMD_Y106G6H.9
    SMD_Y22F5A.5
    SMD_Y47H9C.1
    SMD_Y70C5C.2
    SMD_ZK218.4
    SMD_ZK285.1
    SMD_ZK6.11
    SMD_ZK662.1
    SMD_ZK783.2
  Gene: WBGene00014030
    WBGene00015449
    WBGene00014669
    WBGene00015676
    WBGene00007528
    WBGene00015772
    WBGene00007605
    WBGene00007626
    WBGene00015927
    WBGene00005832
    WBGene00016283
    WBGene00016333
    WBGene00007864
    WBGene00007969
    WBGene00016535
    WBGene00016720
    WBGene00008229
    WBGene00008333
    WBGene00008336
    WBGene00016995
    WBGene00008390
    WBGene00017149
    WBGene00017160
    WBGene00017166
    WBGene00001158
    WBGene00017200
    WBGene00004358
    WBGene00000666
    WBGene00003562
    WBGene00017443
    WBGene00000673
    WBGene00008891
    WBGene00000684
    WBGene00003162
    WBGene00009008
    WBGene00009048
    WBGene00009049
    WBGene00017719
    WBGene00017751
    WBGene00005076
    WBGene00017765
    WBGene00017975
    WBGene00009340
    WBGene00009349
    WBGene00000775
    WBGene00002253
    WBGene00018250
    WBGene00018317
    WBGene00018354
    WBGene00018358
    WBGene00249817
    WBGene00018426
    WBGene00009710
    WBGene00009778
    WBGene00018519
    WBGene00018603
    WBGene00018840
    WBGene00000677
    WBGene00001813
    WBGene00000733
    WBGene00003549
    WBGene00019214
    WBGene00001391
    WBGene00010566
    WBGene00010574
    WBGene00010575
    WBGene00019471
    WBGene00003995
    WBGene00010679
    WBGene00001684
    WBGene00003124
    WBGene00010759
    WBGene00010790
    WBGene00002271
    WBGene00019963
    WBGene00019978
    WBGene00011164
    WBGene00011330
    WBGene00000719
    WBGene00001497
    WBGene00020457
    WBGene00020459
    WBGene00306000
    WBGene00011844
    WBGene00050934
    WBGene00020569
    WBGene00020575
    WBGene00011894
    WBGene00002260
    WBGene00012007
    WBGene00012025
    WBGene00005599
    WBGene00001692
    WBGene00001702
    WBGene00021072
    WBGene00021078
    WBGene00013624
    WBGene00013721
    WBGene00003091
    WBGene00012947
    WBGene00013493
    WBGene00013938
    WBGene00006234
    WBGene00022645
    WBGene00007284
    WBGene00022816
    WBGene00022817
  Attribute_of: Microarray_experiment: WBPaper00026952:N2b_vs_lin-4b
      WBPaper00026952:N2_vs_lin-14(n179ts)
      WBPaper00026952:N2c_vs_lin-4c
      WBPaper00026952:N2_vs_lin-14(n179ts)_rep2
      WBPaper00026952:N2a_vs_lin-4a
  Regulation: Regulated_by_gene: WBGene00003003
      WBGene00002993