Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.16.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93496	0.617
27DAP/17DAP	2.22946	0.263
39DAP/27DAP	1.01835	0.798
41DAP/39DAP	0.90498	0.586
42DAP/41DAP	1.04814	1
43DAP/42DAP	1.14242	0.991
47DAP/43DAP	1.16442	0.779
52DAP/47DAP	1.9821	0.225
57DAP/52DAP	0.94002	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76461	0.028
17DAP/reference	0.88677	0.043
27DAP/reference	0.87524	0.109
39DAP/reference	0.91188	0.228
41DAP/reference	0.87774	0.049
42DAP/reference	0.90968	0.024
43DAP/reference	0.91502	0.222
47DAP/reference	0.90955	0.055
52DAP/reference	0.7846	0.028
57DAP/reference	0.93474	0.34

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00607	0.847
27DAP/17DAP	1.08963	0.751
39DAP/27DAP	0.76543	0.173
41DAP/39DAP	1.29846	0.439
42DAP/41DAP	0.66677	0.14
43DAP/42DAP	1.21427	0.273
47DAP/43DAP	1.34044	0.257
52DAP/47DAP	1.25483	0.66
57DAP/52DAP	2.0964	0.029
57DAP/7DAP	1.3691	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11767	0.613
17DAP/reference	1.02599	1
27DAP/reference	1.08155	0.049
39DAP/reference	1.10635	0.059
41DAP/reference	1.06851	0.539
42DAP/reference	1.23565	0.046
43DAP/reference	1.08261	0.241
47DAP/reference	1.12582	0.791
52DAP/reference	1.2337	0.021
57DAP/reference	1.04121	0.612

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79408	0.012
17DAP/reference	0.71424	0.004
27DAP/reference	0.75001	0.036
39DAP/reference	0.66962	0.008
41DAP/reference	0.86643	0.127
42DAP/reference	0.80298	0.03
43DAP/reference	0.74401	0.013
47DAP/reference	0.86555	0.021
52DAP/reference	0.72879	0.003
57DAP/reference	0.64804	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20616	0.069
17DAP/reference	1.07415	0.394
27DAP/reference	1.08269	0.34
39DAP/reference	1.283	0.018
41DAP/reference	1.02108	0.818
42DAP/reference	1.06985	0.566
43DAP/reference	0.90387	0.179
47DAP/reference	0.91913	0.132
52DAP/reference	0.87526	0.327
57DAP/reference	1.19989	0.501

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.15139	0.966
26DAP/20DAP	0.71484
34DAP/26DAP	1.68076	0.819
51DAP/34DAP	1.07194	0.927
52DAP/51DAP	1.39613	0.742
53DAP/52DAP	1.36317	0.594
55DAP/53DAP	1.18246	0.813
57DAP/55DAP	0.77149	0.213
62DAP/57DAP	1.0515	0.902
68DAP/62DAP	1.26165	0.523
68DAP/14DAP	1.20406	0.328

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81311	0.358

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.0934	0.058
Mature Green Tomato/Ripe Tomato	0.20286	0.017
Immature Eggplant/Mature Eggplant	0.41633	0.062
Ripe Pepper/Ripe Tomato	1.79182	1
Mature Eggplant/Ripe Tomato	2.99978	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94654	0.605
1-1-2/M82	0.74346
12-2/M82	0.88535
12-4/M82	1.10807	1
1-3/M82	0.64406
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.2141	0.695
3-2/M82	N/A	N/A
4-1-1/M82	1.09644	1
4-1/M82	0.92509
4-3-2/M82	0.78795
4-3/M82	1.23352	0.268
5-3/M82	0.9575	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.99561
9-3-2/M82	0.73353

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	2.39741	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92681	1
DC3000/delta hrp 6h	0.96678	0.95
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.83208	0.06

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.52585
DC3000 delta B/DC3000 delta AB	1.82938

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98328	1
Exp 36h	0.75241	0.456
Exp 60h	0.73168	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.10654	1
Var 0h	1.21481	0.936
Var 12h I row2-row1	1.25988	0.473
Var 12h NI row2-row1	0.69548	1
Var 36h I row2-row1	1.11521	1
Var 36h NI row2-row1	0.63936	1
Var 60h I row2-row1	0.89266	0.832
Var 60h NI row2-row1	0.97899	1
Time course 0hI-0hNI	1.35163	0.662
Time course 12hI-12hNI	1.06002	0.684
Time course 36hI-36hNI	3.88893	0.017
Time course 60hI-60hNI	14.8883	0.008

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)	1.19386	0.654
transgenic ySAMdc/azygous control (breaker)	1.66707	0.178
transgenic ySAMdc/azygous control (red)	1.01834	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.85535	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.17519	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	10.9776	0.083
Manapal/WT (break)	4.39466	0.123
Manapal/WT (red)	1.61463	1