Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.4.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95896	0.713
27DAP/17DAP	1.10518	1
39DAP/27DAP	0.96879	0.769
41DAP/39DAP	0.64143	0.12
42DAP/41DAP	0.9344	1
43DAP/42DAP	1.16007	0.976
47DAP/43DAP	1.11125	0.965
52DAP/47DAP	1.01225	0.908
57DAP/52DAP	0.97623	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82067	0.089
17DAP/reference	0.88999	0.26
27DAP/reference	0.89869	0.275
39DAP/reference	1.05068	0.816
41DAP/reference	0.85328	0.114
42DAP/reference	0.93502	0.124
43DAP/reference	0.93552	0.429
47DAP/reference	1.00733	0.72
52DAP/reference	1.0229	0.709
57DAP/reference	1.08634	0.321

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95592	0.644
27DAP/17DAP	1.3547	0.295
39DAP/27DAP	0.86669	0.334
41DAP/39DAP	1.12308	0.748
42DAP/41DAP	0.76594	0.06
43DAP/42DAP	1.09089	0.351
47DAP/43DAP	0.877	0.597
52DAP/47DAP	1.12244	0.789
57DAP/52DAP	1.22066	0.451
57DAP/7DAP	0.89954	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25617	0.235
17DAP/reference	1.07683	0.399
27DAP/reference	1.23703	0.03
39DAP/reference	0.97956	0.552
41DAP/reference	1.18416	0.507
42DAP/reference	1.09468	0.889
43DAP/reference	1.20511	0.024
47DAP/reference	1.19774	0.324
52DAP/reference	1.23788	0.375
57DAP/reference	0.95962	0.426

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87005	0.119
17DAP/reference	0.73864	0.018
27DAP/reference	0.98337	0.619
39DAP/reference	0.98754	0.554
41DAP/reference	0.88242	0.145
42DAP/reference	0.88664	0.121
43DAP/reference	0.88141	0.157
47DAP/reference	0.83866	0.055
52DAP/reference	0.84945	0.143
57DAP/reference	0.86279	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08856	0.575
17DAP/reference	0.96212	0.592
27DAP/reference	1.25046	0.088
39DAP/reference	1.0907	0.563
41DAP/reference	1.2021	0.286
42DAP/reference	0.91589	0.552
43DAP/reference	1.13143	0.894
47DAP/reference	0.92634	0.421
52DAP/reference	0.98703	0.781
57DAP/reference	0.98631	0.633

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9596	1
26DAP/20DAP	1.15437	0.924
34DAP/26DAP	0.80358	0.479
51DAP/34DAP	1.25912	0.073
52DAP/51DAP	1.16167	0.404
53DAP/52DAP	1.10217	0.91
55DAP/53DAP	1.02399	0.964
57DAP/55DAP	0.7743	0.322
62DAP/57DAP	1.13932	0.393
68DAP/62DAP	0.90821	0.769
68DAP/14DAP	1.2441	0.694

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.72118	0.036

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.62928	0.226
Mature Green Tomato/Ripe Tomato	1.05827
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.94298	0.358
1-3/M82	N/A	N/A
2-1-1/M82	0.76962
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.72305
5-3/M82	1.23132
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

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	0.87232	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	1.15297	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98261	1
DC3000/delta hrp 6h	0.71636	0.95
DC3000/delta hrp 12h	1.11866
DC3000/delta hrp 24h	0.91503	0.84

Experiment: DC3000 effector mutants

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

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.038	1
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	0.91693	0.627
Var 12h NI row2-row1	1.00946	1
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	1.4916	1
Var 60h I row2-row1	1.02429
Var 60h NI row2-row1	0.97925	1
Time course 0hI-0hNI	0.97447	0.958
Time course 12hI-12hNI	1.02982	0.827
Time course 36hI-36hNI	1.06228	0.58
Time course 60hI-60hNI	0.78788	0.047

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)	0.97214	0.662
transgenic ySAMdc/azygous control (breaker)	1.73265	0.166
transgenic ySAMdc/azygous control (red)	1.07538	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0032	0.811

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77787	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.12083	1
Manapal/WT (break)	0.80764	0.333
Manapal/WT (red)	0.78405	0.424