Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.13.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03909	0.851
27DAP/17DAP	1.3478	0.73
39DAP/27DAP	1.51658	0.382
41DAP/39DAP	1.02202	0.929
42DAP/41DAP	0.75179	0.397
43DAP/42DAP	1.00542	0.945
47DAP/43DAP	0.78079	0.33
52DAP/47DAP	1.74237	0.233
57DAP/52DAP	0.765	0.673

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94781	0.167
17DAP/reference	1.03941	0.089
27DAP/reference	1.02969	0.394
39DAP/reference	1.00271	1
41DAP/reference	0.90629	0.154
42DAP/reference	1.02453	0.449
43DAP/reference	0.90134	0.103
47DAP/reference	0.99972	0.764
52DAP/reference	1.01966	1
57DAP/reference	0.96228	0.308

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89384	0.201
27DAP/17DAP	1.00256	1
39DAP/27DAP	1.032	0.643
41DAP/39DAP	1.11605	0.427
42DAP/41DAP	0.91693	0.3
43DAP/42DAP	1.12958	0.018
47DAP/43DAP	1.08717	0.227
52DAP/47DAP	0.95571	0.824
57DAP/52DAP	1.15452	0.368
57DAP/7DAP	1.15962	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44053	0.027
17DAP/reference	1.4706	0.006
27DAP/reference	1.33495	0.012
39DAP/reference	1.45531	0.006
41DAP/reference	1.39351	0.016
42DAP/reference	1.55048	0.01
43DAP/reference	1.88003	0.006
47DAP/reference	1.2218	0.44
52DAP/reference	1.41814	0.008
57DAP/reference	1.31595	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0139	0.823
17DAP/reference	1.00032	0.924
27DAP/reference	0.9225	0.304
39DAP/reference	1.00839	0.745
41DAP/reference	1.12135	0.335
42DAP/reference	0.97707	0.392
43DAP/reference	0.8928	0.111
47DAP/reference	1.02014	0.603
52DAP/reference	0.94732	0.043
57DAP/reference	0.99203	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22431	0.09
17DAP/reference	1.0294	0.977
27DAP/reference	1.447	0.067
39DAP/reference	1.09844	0.733
41DAP/reference	1.298	0.01
42DAP/reference	1.28232	0.258
43DAP/reference	1.2344	0.233
47DAP/reference	0.93069	0.231
52DAP/reference	1.6958	0.062
57DAP/reference	0.80051	0.048

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94269	0.89
26DAP/20DAP	0.99669	1
34DAP/26DAP	0.93762	0.539
51DAP/34DAP	1.04511	0.496
52DAP/51DAP	1.03505	0.638
53DAP/52DAP	1.07765	0.47
55DAP/53DAP	0.95952	0.515
57DAP/55DAP	1.12115	0.906
62DAP/57DAP	1.03036	0.8
68DAP/62DAP	1.08775	0.885
68DAP/14DAP	1.59125	0.236

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.38394	0.018

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.90357	0.063
Mature Green Tomato/Ripe Tomato	0.43013	0.021
Immature Eggplant/Mature Eggplant	0.89606	0.651
Ripe Pepper/Ripe Tomato	0.14443	0.224
Mature Eggplant/Ripe Tomato	0.14556	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02803	1
1-1-2/M82	1.0903	1
12-2/M82	0.95465	0.955
12-4/M82	0.91676	1
1-3/M82	1.06114	1
2-1-1/M82	1.0204	1
2-1/M82	N/A	N/A
2-6/M82	0.94289	1
3-2/M82	1.0799	0.549
4-1-1/M82	0.75173	0.959
4-1/M82	0.97469
4-3-2/M82	0.9103	1
4-3/M82	0.72598	0.72
5-3/M82	1.34487	1
6-2/M82	1.21348	1
6-3/M82	1.00304	1
7-1/M82	1.14471
7-2/M82	1.12995	1
9-3-2/M82	0.75184	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.7329	0.321
IL2-6/WTpooled	0.99316	1
IL7-5/WTpooled	0.8799	1
IL7-3/WTpooled	0.79124	0.418
IL12-4/WTpooled	0.91698	1
IL1-4/WTpooled	0.77919	0.562
WT/WTpooled	1.07378	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	1.73027	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02378	0.921
DC3000/delta hrp 6h	1.15882	1
DC3000/delta hrp 12h	1.12408	1
DC3000/delta hrp 24h	1.07477	0.516

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.34054	0.042
DC3000 delta B/DC3000 delta AB	1.25746	0.17

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.06551	1
Exp 60h	1.23291	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01495	1
Var 0h	1.08587	0.311
Var 12h I row2-row1	1.26615	0.216
Var 12h NI row2-row1	1.00529	1
Var 36h I row2-row1	1.11931	1
Var 36h NI row2-row1	0.85032	0.549
Var 60h I row2-row1	1.31642	0.562
Var 60h NI row2-row1	1.2679	1
Time course 0hI-0hNI	1.08885	0.852
Time course 12hI-12hNI	1.04283	0.824
Time course 36hI-36hNI	1.04661	0.722
Time course 60hI-60hNI	2.38947	0.009

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)	1.40672	0.384
transgenic ySAMdc/azygous control (breaker)	0.95623	0.173
transgenic ySAMdc/azygous control (red)	0.95378	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98699	0.295

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86616	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.19093	0.105
Manapal/WT (break)	0.56617	0.333
Manapal/WT (red)	0.77465	0.181