TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv1981c/nrdF1:

update plot	correlation	link to info on gene
Rv3738c/PPE66	(cc=0.6569)	info on Rv3738c/PPE66
Rv0872c/PE_PGRS15	(cc=0.5792)	info on Rv0872c/PE_PGRS15
Rv1503c/-	(cc=0.5223)	info on Rv1503c/-
Rv2777c/-	(cc=0.5204)	info on Rv2777c/-
Rv3158/nuoN	(cc=0.5191)	info on Rv3158/nuoN
Rv2459/-	(cc=0.5148)	info on Rv2459/-
Rv2954c/-	(cc=0.5056)	info on Rv2954c/-
Rv0114/gmhB	(cc=0.5018)	info on Rv0114/gmhB
Rv2276/cyp121	(cc=0.4983)	info on Rv2276/cyp121
Rv3232c/ppk2	(cc=0.4961)	info on Rv3232c/ppk2

Correlation of Rv1981c/nrdF1 with Rv0872c/PE_PGRS15

Normalized LFCs for Rv1981c/nrdF1:
(description and provenance of datasets)

	Rv1981c/nrdF1	Rv0872c/PE_PGRS15
Fe_supp_jason_reseq	0.204	0.14
low_pH_jason_reseq	-1.022	-1.631
NO_jason_reseq	-0.417	-0.32
B6_jason_reseq	0.31	0.24
MHCII_jason_reseq	0.087	0.762
Isoniazid02	-0.639	-0.473
Rifampicin4	0.143	0.671
Ethambutol3	0.064	-0.406
Meropenem3	-0.466	0.059
Vancomycin16	-0.456	-0.194
Rv2680_day32	0.742	0.061
H37Rv_KO_MarP	-0.333	-0.045
hypoxia_3wks	-0.646	-0.175
hypoxia_6wks	-1.297	-0.76
glycerol	0.089	0.581
cholesterol	-0.384	0.441
AJ	-0.012	0.197
Bibs02	0.468	0.228
Bibs02c	0.473	0.782
BL6	0.25	0.332
BL6a	0.443	0.74
BXD01	0.283	0.276
BXD010	0.295	-0.058
BXD011	0.653	-0.107
BXD03	0.455	0.133
BXD04	0.492	-0.047
BXD05	0.397	0.468
BXD06	0.536	-0.06
BXD07	0.277	0.117
BXD08	-0.029	0.412
BXD09	0.417	0.148
CAST	-0.012	0.637
CCcont	0.321	0.106
DS01	0.301	-0.161
DS02	-0.028	0.17
DS04	0.025	0.447
DS0c	0.542	-0.218
GP01	0.421	0.25
GP02	0.603	0.146
GP0c	0.365	-0.039
NOD	0.667	0.236
NZO	-0.39	-0.201
PWK	0.036	-0.104
H37Rv_KO_CtpC	0.101	0.265
H37Rv_KO_CtpD	0.44	0.351
H37Rv_KO_Rv1272	0.588	0.952
H37Rv_KO_SugABC	1.0	0.895
H37Rv_KO_MbtN	0.046	0.369
Trans05	0.555	0.419
macrophage_unactivated	0.174	1.004
IL1	0.294	0.225
Rapamycin	-0.157	0.847
Tcell	0.111	0.534
GMCSF	0.269	0.069
IFNab	0.166	0.378
IFNg	0.059	0.313
IFNg_GMCSF1	0.273	0.214
Rv1432_day32	-0.155	0.272
Rv1565c_day32	-0.878	-0.351
secA2_input	-0.427	0.094
delta_Rv3594	-0.049	-0.162
delta_Rv3717	-0.31	-0.646
delta_Rv3811	0.012	-0.47
delta_Rv0954	0.231	-0.885
PonA1	0.359	-0.247
EccD1_KO	0.066	0.02
EspI_KO	0.103	-0.128
PE35_KO	-0.108	-0.248
PPE68_KO	0.032	-0.294
glycerol2	0.965	1.338
lignocerate	0.958	1.169
oleate	1.048	1.262
phosphatidylcholine	0.957	1.195
acetate	0.258	0.281
glucAc	0.183	0.554
Rv0950ko	0.663	0.208
Rv1096ko	0.118	0.208
Rv3684ko	-0.331	0.226
delta_otsA_trehalose	0.71	-0.152