Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.20.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14415	0.725
27DAP/17DAP	1.0123	1
39DAP/27DAP	0.9929	0.663
41DAP/39DAP	0.91112	0.617
42DAP/41DAP	0.80766	1
43DAP/42DAP	0.9895	0.925
47DAP/43DAP	1.15592	0.595
52DAP/47DAP	1.52379	0.654
57DAP/52DAP	1.02668	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8661	0.149
17DAP/reference	1.24822	0.083
27DAP/reference	1.07714	0.478
39DAP/reference	1.21437	0.218
41DAP/reference	0.94692	0.542
42DAP/reference	0.78446	0.01
43DAP/reference	0.88632	0.259
47DAP/reference	0.84684	0.011
52DAP/reference	0.7789	0.024
57DAP/reference	0.78547	0.042

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18487	0.201
27DAP/17DAP	0.9492	0.887
39DAP/27DAP	1.07741	0.845
41DAP/39DAP	1.05229	0.88
42DAP/41DAP	0.84895	0.365
43DAP/42DAP	0.65165	0.022
47DAP/43DAP	1.00176	0.989
52DAP/47DAP	1.22289	0.573
57DAP/52DAP	1.04138	1
57DAP/7DAP	0.83833	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94462	0.402
17DAP/reference	0.91436	0.253
27DAP/reference	0.7866	0.031
39DAP/reference	0.94243	0.307
41DAP/reference	0.62044	0.024
42DAP/reference	0.72671	0.012
43DAP/reference	0.85595	0.086
47DAP/reference	0.85254	0.128
52DAP/reference	1.05466	0.802
57DAP/reference	0.88338	0.09

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98401	0.736
17DAP/reference	0.87563	0.253
27DAP/reference	0.82257	0.074
39DAP/reference	0.86186	0.136
41DAP/reference	0.84569	0.108
42DAP/reference	0.78536	0.042
43DAP/reference	0.91803	0.32
47DAP/reference	1.10246	0.426
52DAP/reference	0.80338	0.015
57DAP/reference	1.10416	0.755

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90451	0.214
17DAP/reference	0.82705	0.077
27DAP/reference	0.92755	0.27
39DAP/reference	0.93347	0.163
41DAP/reference	0.928	0.293
42DAP/reference	0.91149	0.361
43DAP/reference	0.86403	0.246
47DAP/reference	0.80815	0.027
52DAP/reference	1.25944	0.801
57DAP/reference	0.74232	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.20449	0.966
26DAP/20DAP	1.13041	1
34DAP/26DAP	1.25726	0.154
51DAP/34DAP	1.51769	0.089
52DAP/51DAP	0.94297	1
53DAP/52DAP	1.15338	0.688
55DAP/53DAP	1.06545	0.79
57DAP/55DAP	1.53776	0.164
62DAP/57DAP	0.79254	0.28
68DAP/62DAP	1.05103	0.914
68DAP/14DAP	1.41833	0.249

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.41122	0.036

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	6.09336	0.058
Mature Green Tomato/Ripe Tomato	2.27427	0.437
Immature Eggplant/Mature Eggplant	1.25836	0.065
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	2.48689

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.79195
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
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	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	1.39478	1
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	0.89328	0.321
IL2-6/WTpooled	1.0717	0.584
IL7-5/WTpooled	1.4364	0.792
IL7-3/WTpooled	0.82916	0.31
IL12-4/WTpooled	1.04022	1
IL1-4/WTpooled	0.95692	0.562
WT/WTpooled	0.92134	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	2.10617	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.93655	0.95
DC3000/delta hrp 12h	1.07095	1
DC3000/delta hrp 24h	1.54659	0.356

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	0.90487	0.213
Exp 36h	1.11865	0.693
Exp 60h	0.98581	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01864	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.05049	0.795
Var 12h NI row2-row1	1.08274	1
Var 36h I row2-row1	1.14588	0.908
Var 36h NI row2-row1	0.61679	0.645
Var 60h I row2-row1	0.95898	0.582
Var 60h NI row2-row1	0.98726	1
Time course 0hI-0hNI	0.84931	0.418
Time course 12hI-12hNI	1.11869	0.367
Time course 36hI-36hNI	0.9296	0.403
Time course 60hI-60hNI	1.73077	0.069

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)	0.92931	0.409
transgenic ySAMdc/azygous control (breaker)	0.96782	0.49
transgenic ySAMdc/azygous control (red)	1.03809	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.63842	0.042

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.06954	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95054	1
Manapal/WT (break)	0.80835	0.333
Manapal/WT (red)	0.69541	0.181