Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.19.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08256	0.893
27DAP/17DAP	1.06476	1
39DAP/27DAP	0.91394	0.583
41DAP/39DAP	1.05757	0.67
42DAP/41DAP	1.08571	0.954
43DAP/42DAP	0.94434	0.883
47DAP/43DAP	1.2534	0.481
52DAP/47DAP	1.05244	0.934
57DAP/52DAP	1.18167	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19123	0.11
17DAP/reference	1.21044	0.132
27DAP/reference	1.234	0.15
39DAP/reference	1.10476	0.286
41DAP/reference	1.15389	0.111
42DAP/reference	1.26731	0.001
43DAP/reference	1.02543	0.928
47DAP/reference	1.11176	0.096
52DAP/reference	1.11563	0.217
57DAP/reference	0.92332	0.262

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04805	0.515
27DAP/17DAP	1.04817	0.852
39DAP/27DAP	1.04356	0.672
41DAP/39DAP	0.94269	0.747
42DAP/41DAP	1.08126	0.415
43DAP/42DAP	1.04534	0.627
47DAP/43DAP	1.02354	0.92
52DAP/47DAP	1.18191	0.428
57DAP/52DAP	1.18009	0.303
57DAP/7DAP	1.07004	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25467	0.185
17DAP/reference	1.60583	0.007
27DAP/reference	1.69026	0.006
39DAP/reference	1.4268	0.391
41DAP/reference	1.59872	0.037
42DAP/reference	1.70819	0.009
43DAP/reference	1.40175	0.056
47DAP/reference	1.16589	0.279
52DAP/reference	1.21731	0.086
57DAP/reference	1.25906	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32767	0.053
17DAP/reference	1.48495	0.066
27DAP/reference	1.21387	0.131
39DAP/reference	1.14893	0.066
41DAP/reference	1.19725	0.109
42DAP/reference	1.08588	0.583
43DAP/reference	1.40604	0.205
47DAP/reference	0.97837	0.5
52DAP/reference	1.38362	0.038
57DAP/reference	1.53428	0.026

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31815	0.053
17DAP/reference	1.08752	0.572
27DAP/reference	1.20908	0.105
39DAP/reference	1.01028	0.935
41DAP/reference	1.27937	0.012
42DAP/reference	1.59264	0.009
43DAP/reference	1.50457	0.008
47DAP/reference	1.18625	0.099
52DAP/reference	1.82133	0.06
57DAP/reference	1.0506	0.878

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85109	1
26DAP/20DAP	0.9729	1
34DAP/26DAP	1.1637	0.819
51DAP/34DAP	1.01038	1
52DAP/51DAP	1.20876	0.207
53DAP/52DAP	0.84441	0.06
55DAP/53DAP	1.10772	0.608
57DAP/55DAP	1.00238	0.923
62DAP/57DAP	1.14719	0.8
68DAP/62DAP	1.21251	0.977
68DAP/14DAP	0.92791	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.70359	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.80012	0.148
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.51265	0.224
Mature Eggplant/Ripe Tomato	0.26632	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.13494	0.574
1-1-2/M82	1.14935	1
12-2/M82	1.2116	1
12-4/M82	0.95892
1-3/M82	1.12246
2-1-1/M82	N/A	N/A
2-1/M82	0.5358	0.322
2-6/M82	1.33101
3-2/M82	1.04684	0.463
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.45981	0.487
4-3/M82	0.48411
5-3/M82	1.1077	1
6-2/M82	1.8396	0.253
6-3/M82	1.05381	1
7-1/M82	0.72894	0.803
7-2/M82	0.84339	0.881
9-3-2/M82	1.01141

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.33	0.277
IL2-6/WTpooled	0.85408	0.473
IL7-5/WTpooled	0.92356	1
IL7-3/WTpooled	1.49303	1
IL12-4/WTpooled	0.8992	0.71
IL1-4/WTpooled	1.23594	1
WT/WTpooled	1.00967	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	0.90577	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91436	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.07662	1
DC3000/delta hrp 24h	1.20955	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.90486	0.273
DC3000 delta B/DC3000 delta AB	1.081	0.443

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95316	1
Exp 36h	1.0901	1
Exp 60h	0.8896	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00156	1
Var 0h	0.93193	1
Var 12h I row2-row1	0.8945	0.705
Var 12h NI row2-row1	0.94347	0.713
Var 36h I row2-row1	0.94685	1
Var 36h NI row2-row1	1.13398	1
Var 60h I row2-row1	1.0571	1
Var 60h NI row2-row1	1.03314	1
Time course 0hI-0hNI	1.10463	0.764
Time course 12hI-12hNI	0.97832	0.847
Time course 36hI-36hNI	0.89019	0.096
Time course 60hI-60hNI	0.42349	0.005

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)	0.86764	0.3
transgenic ySAMdc/azygous control (breaker)	1.99786	0.161
transgenic ySAMdc/azygous control (red)	1.26184	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91281	0.043

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87144	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.17916	1