Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.2.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95183	0.683
27DAP/17DAP	2.153	0.111
39DAP/27DAP	2.8668	0.307
41DAP/39DAP	1.1629	0.802
42DAP/41DAP	1.0763	0.967
43DAP/42DAP	0.90552	0.829
47DAP/43DAP	1.50069	0.563
52DAP/47DAP	0.79942	0.502
57DAP/52DAP	1.11372	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.41306	0.024
17DAP/reference	0.58713	0.009
27DAP/reference	0.61838	0.021
39DAP/reference	0.52341	0.014
41DAP/reference	0.58109	0.014
42DAP/reference	0.64875	0.001
43DAP/reference	0.97847	0.708
47DAP/reference	0.6604	0.001
52DAP/reference	0.52696	0.014
57DAP/reference	0.71473	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04755	1
27DAP/17DAP	0.853	0.648
39DAP/27DAP	1.03113
41DAP/39DAP	2.65428	0.018
42DAP/41DAP	0.9122	0.407
43DAP/42DAP	0.35124	0.022
47DAP/43DAP	1.57204	0.027
52DAP/47DAP	1.00006	0.962
57DAP/52DAP	0.74697	0.235
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.51497	0.059
17DAP/reference	0.64498	0.02
27DAP/reference	0.83772	0.215
39DAP/reference	0.49266	0.011
41DAP/reference	0.61305	0.013
42DAP/reference	0.66518	0.029
43DAP/reference	0.73803	0.012
47DAP/reference	0.58479	0.057
52DAP/reference	0.8825	0.126
57DAP/reference	0.66862	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.56212	0.016
17DAP/reference	0.42813	0.003
27DAP/reference	0.52368	0.018
39DAP/reference	0.59337	0.02
41DAP/reference	0.60916	0.014
42DAP/reference	0.6318	0.014
43DAP/reference	0.73383	0.072
47DAP/reference	0.70252	0.018
52DAP/reference	0.46605	0.003
57DAP/reference	0.75861	0.021

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.4671	0.037
17DAP/reference	0.68156	0.143
27DAP/reference	0.57398	0.029
39DAP/reference	0.79047	0.092
41DAP/reference	0.76924	0.064
42DAP/reference	0.65133	0.019
43DAP/reference	0.59072	0.024
47DAP/reference	0.48588	0.006
52DAP/reference	0.74198	0.204
57DAP/reference	0.55181	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05142	0.966
26DAP/20DAP	0.86616	1
34DAP/26DAP	0.62366	0.112
51DAP/34DAP	1.00881	0.988
52DAP/51DAP	0.57198
53DAP/52DAP	0.86483	0.587
55DAP/53DAP	1.14736	0.948
57DAP/55DAP	1.17161	0.826
62DAP/57DAP	1.10715	0.868
68DAP/62DAP	0.75594	0.245
68DAP/14DAP	0.71628	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.6881	0.052

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.27956	0.068
Mature Green Tomato/Ripe Tomato	2.36249	0.023
Immature Eggplant/Mature Eggplant	3.58037	0.05
Ripe Pepper/Ripe Tomato	3.82374	0.258
Mature Eggplant/Ripe Tomato	1.13279	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.99219
12-2/M82	N/A	N/A
12-4/M82	0.6377
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	0.841	1
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	1.91426	0.572
6-2/M82	6.05852
6-3/M82	0.62271
7-1/M82	N/A	N/A
7-2/M82	2.16209	0.324
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	1.23722	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.84108	0.31
IL12-4/WTpooled	1.07785	0.646
IL1-4/WTpooled	0.90306
WT/WTpooled	0.94963	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	1.22319	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0849	0.914
DC3000/delta hrp 6h	1.05803	1
DC3000/delta hrp 12h	1.08605	1
DC3000/delta hrp 24h	2.4311	0.028

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.52439	0.042
DC3000 delta B/DC3000 delta AB	5.51351	0.019

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.68109	0.254
Exp 36h	1.94043	0.489
Exp 60h	2.72569	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.22145	1
Var 0h	1.16855	0.594
Var 12h I row2-row1	0.90229	0.77
Var 12h NI row2-row1	2.51909	0.649
Var 36h I row2-row1	1.59281	0.298
Var 36h NI row2-row1	0.53086	0.478
Var 60h I row2-row1	1.0165	1
Var 60h NI row2-row1	0.59134	0.318
Time course 0hI-0hNI	1.75004	0.297
Time course 12hI-12hNI	1.19336	0.82
Time course 36hI-36hNI	3.75713	0.004
Time course 60hI-60hNI	91.8051	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)	1.30498	0.541
transgenic ySAMdc/azygous control (breaker)	0.92617	0.49
transgenic ySAMdc/azygous control (red)	1.01325	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97162	0.168

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.73244	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.94103	0.307
Manapal/WT (break)	2.56977	0.381
Manapal/WT (red)	1.05815	1