Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.10.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15316	0.786
27DAP/17DAP	0.42509	0.027
39DAP/27DAP	0.60744	0.257
41DAP/39DAP	0.60894	0.055
42DAP/41DAP	0.66233	0.397
43DAP/42DAP	1.4506	0.346
47DAP/43DAP	0.35779	0.049
52DAP/47DAP	1.15829	0.818
57DAP/52DAP	1.26395	0.849

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74873	0.098
17DAP/reference	0.46641	0.008
27DAP/reference	0.41146	0.012
39DAP/reference	0.38663	0.012
41DAP/reference	0.2041	0.008
42DAP/reference	0.25774	0.001
43DAP/reference	0.11683	0.008
47DAP/reference	0.10473	0.001
52DAP/reference	0.08426	0.008
57DAP/reference	0.12066	0.006

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.98533	0.039
27DAP/17DAP	0.68643	0.187
39DAP/27DAP	0.24168	0.028
41DAP/39DAP	1.48576	0.258
42DAP/41DAP	0.94368	0.63
43DAP/42DAP	0.33091	0.02
47DAP/43DAP	0.6917	0.098
52DAP/47DAP	1.11281	0.724
57DAP/52DAP	1.16511	0.606
57DAP/7DAP	0.60698	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16379	0.292
17DAP/reference	0.85451	0.049
27DAP/reference	0.51795	0.01
39DAP/reference	0.40536	0.011
41DAP/reference	0.27914	0.009
42DAP/reference	0.2178	0.01
43DAP/reference	0.24326	0.009
47DAP/reference	0.19882	0.026
52DAP/reference	0.31944	0.01
57DAP/reference	0.35208	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.4267	0.009
17DAP/reference	0.46866	0.012
27DAP/reference	0.54589	0.038
39DAP/reference	0.28733	0.008
41DAP/reference	0.3191	0.005
42DAP/reference	0.28384	0.01
43DAP/reference	0.13263	0.002
47DAP/reference	0.1783	0.007
52DAP/reference	0.16982	0.003
57DAP/reference	0.09364	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.55513	0.016
17DAP/reference	1.94643	0.105
27DAP/reference	1.56212	0.033
39DAP/reference	1.19816	0.307
41DAP/reference	0.73223	0.046
42DAP/reference	0.43918	0.018
43DAP/reference	0.57291	0.016
47DAP/reference	0.26236	0.004
52DAP/reference	0.60111	0.197
57DAP/reference	1.26021	0.73

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.25931	0.966
26DAP/20DAP	1.24701	0.297
34DAP/26DAP	0.84975	0.399
51DAP/34DAP	0.36934	0.049
52DAP/51DAP	0.95143	1
53DAP/52DAP	0.55281	0.049
55DAP/53DAP	0.69431	0.203
57DAP/55DAP	0.72101	0.076
62DAP/57DAP	2.04999	0.002
68DAP/62DAP	1.013	0.863
68DAP/14DAP	0.37995	0.375

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.37553	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.65206	0.058
Mature Green Tomato/Ripe Tomato	11.3522	0.026
Immature Eggplant/Mature Eggplant	0.48644	0.062
Ripe Pepper/Ripe Tomato	48.35	0.258
Mature Eggplant/Ripe Tomato	52.4552	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.82554	0.958
12-2/M82	0.50493	0.619
12-4/M82	0.81749
1-3/M82	N/A	N/A
2-1-1/M82	0.87718
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.1775	0.967
4-1-1/M82	1.03074
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.78378
5-3/M82	1.83219	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.98936
7-2/M82	0.83128
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.14396	1
IL2-6/WTpooled	0.75446	1
IL7-5/WTpooled	1.5023	0.792
IL7-3/WTpooled	1.33705	0.362
IL12-4/WTpooled	0.95904	0.71
IL1-4/WTpooled	1.12014	0.426
WT/WTpooled	1.02053	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	0.99721	1

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98259	1
DC3000/delta hrp 6h	1.03448	1
DC3000/delta hrp 12h	0.92867	1
DC3000/delta hrp 24h	1.05829	0.383

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05237	0.313
DC3000 delta B/DC3000 delta AB	0.58048	0.1

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98221	1
Exp 36h	1.03456	1
Exp 60h	1.07303	1

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.01996	1
Var 0h	1.11652	0.98
Var 12h I row2-row1	1.02774	0.736
Var 12h NI row2-row1	1.03325	1
Var 36h I row2-row1	0.86385	1
Var 36h NI row2-row1	1.00877	1
Var 60h I row2-row1	1.39194	0.562
Var 60h NI row2-row1	0.97042	0.977
Time course 0hI-0hNI	0.9935	1
Time course 12hI-12hNI	1.0237	0.779
Time course 36hI-36hNI	1.03533	0.401
Time course 60hI-60hNI	0.76255	0.161

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.12068	0.798
transgenic ySAMdc/azygous control (breaker)	4.62232	0.161
transgenic ySAMdc/azygous control (red)	1.44805	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.42456	0.07

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8508	0.238

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	31.3948	0.087
Manapal/WT (break)	15.2278	0.123
Manapal/WT (red)	3.21216	0.413