Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.13.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91319	0.522
27DAP/17DAP	1.15194	0.845
39DAP/27DAP	0.70567	0.397
41DAP/39DAP	1.66363	0.352
42DAP/41DAP	0.98602	1
43DAP/42DAP	0.78792	0.705
47DAP/43DAP	0.90272	0.591
52DAP/47DAP	2.36596	0.114
57DAP/52DAP	0.67152	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96911	0.489
17DAP/reference	0.92661	0.053
27DAP/reference	0.93331	0.223
39DAP/reference	0.99973	1
41DAP/reference	1.06942	0.221
42DAP/reference	0.85894	0.006
43DAP/reference	0.9538	0.302
47DAP/reference	0.80231	0.002
52DAP/reference	0.90506	0.189
57DAP/reference	0.8308	0.027

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99072	0.801
27DAP/17DAP	0.98113	0.887
39DAP/27DAP	1.1513	0.378
41DAP/39DAP	1.28681	0.514
42DAP/41DAP	0.94185	0.603
43DAP/42DAP	1.12332	0.103
47DAP/43DAP	1.04342	0.934
52DAP/47DAP	0.96149	0.868
57DAP/52DAP	0.9739	0.745
57DAP/7DAP	1.0512	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84737	0.146
17DAP/reference	0.76263	0.019
27DAP/reference	0.75187	0.01
39DAP/reference	0.68381	0.011
41DAP/reference	0.71665	0.025
42DAP/reference	0.64381	0.01
43DAP/reference	0.63166	0.011
47DAP/reference	0.79883	0.128
52DAP/reference	0.60113	0.012
57DAP/reference	0.63258	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18289	0.319
17DAP/reference	1.16579	0.042
27DAP/reference	1.00143	0.663
39DAP/reference	1.0698	1
41DAP/reference	0.87764	0.074
42DAP/reference	0.87063	0.022
43DAP/reference	1.3705	0.062
47DAP/reference	0.93615	0.05
52DAP/reference	1.05124	0.322
57DAP/reference	1.13461	0.363

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78381	0.061
17DAP/reference	1.0363	1
27DAP/reference	0.7456	0.039
39DAP/reference	0.73693	0.022
41DAP/reference	0.87332	0.209
42DAP/reference	0.80846	0.134
43DAP/reference	0.672	0.024
47DAP/reference	1.04107	0.562
52DAP/reference	0.74032	0.141
57DAP/reference	0.73323	0.065

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.25648	0.945
26DAP/20DAP	0.98542	1
34DAP/26DAP	1.06682	1
51DAP/34DAP	0.9488	0.714
52DAP/51DAP	1.05869	0.776
53DAP/52DAP	1.0393	0.901
55DAP/53DAP	1.06431	0.712
57DAP/55DAP	1.14692	0.543
62DAP/57DAP	1.177	0.35
68DAP/62DAP	0.76415	0.263
68DAP/14DAP	0.77611	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.78497	0.102

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.30529	0.752
Immature Eggplant/Mature Eggplant	2.68678
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.37818

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9475	0.944
1-1-2/M82	0.92586	1
12-2/M82	1.00662	1
12-4/M82	1.11566
1-3/M82	0.78093	0.378
2-1-1/M82	1.08664	0.764
2-1/M82	N/A	N/A
2-6/M82	1.02658	1
3-2/M82	N/A	N/A
4-1-1/M82	1.03914	1
4-1/M82	0.65443
4-3-2/M82	0.84472	1
4-3/M82	0.60786
5-3/M82	0.98188	1
6-2/M82	0.85538	0.497
6-3/M82	0.982	1
7-1/M82	1.05399
7-2/M82	1.07171	1
9-3-2/M82	0.79612

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.97003	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.35764	0.792
IL7-3/WTpooled	0.93113
IL12-4/WTpooled	0.89577	1
IL1-4/WTpooled	0.97759	1
WT/WTpooled	0.95805	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	0.99636

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06107	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.325	1
DC3000/delta hrp 24h	1.17251	0.062

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	1.3757	0.249

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.44067	1
Exp 36h	1.80017	1
Exp 60h	0.87825	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.08505	1
Var 0h	0.57417	0.98
Var 12h I row2-row1	1.13856	0.263
Var 12h NI row2-row1	1.01085	1
Var 36h I row2-row1	0.91827	0.805
Var 36h NI row2-row1	0.89372	0.706
Var 60h I row2-row1	1.43369	0.562
Var 60h NI row2-row1	1.24561	0.904
Time course 0hI-0hNI	1.21803	0.344
Time course 12hI-12hNI	1.04317	0.747
Time course 36hI-36hNI	0.97176	0.45
Time course 60hI-60hNI	1.7581	0.015

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)	1.22982	0.326
transgenic ySAMdc/azygous control (breaker)	1.40101	1
transgenic ySAMdc/azygous control (red)	1.2049	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07289	0.119

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.24477	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.04611	0.09
Manapal/WT (break)	1.11135	1
Manapal/WT (red)	1.65347	0.222