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 Rv2300c/-:

update plot	correlation	link to info on gene
Rv3738c/PPE66	(cc=0.5432)	info on Rv3738c/PPE66
Rv2497c/bkdA	(cc=0.4583)	info on Rv2497c/bkdA
Rv3485c/-	(cc=0.4561)	info on Rv3485c/-
Rv0830/-	(cc=0.4523)	info on Rv0830/-
Rv1141c/echA11	(cc=0.4476)	info on Rv1141c/echA11
Rv0872c/PE_PGRS15	(cc=0.439)	info on Rv0872c/PE_PGRS15
Rv3435c/-	(cc=0.4362)	info on Rv3435c/-
Rv2345/-	(cc=0.4342)	info on Rv2345/-
Rv1153c/omt	(cc=0.43)	info on Rv1153c/omt
Rv3092c/-	(cc=0.4259)	info on Rv3092c/-

Correlation of Rv2300c/- with Rv0872c/PE_PGRS15

Normalized LFCs for Rv2300c/-:
(description and provenance of datasets)

	Rv2300c/-	Rv0872c/PE_PGRS15
Fe_supp_jason_reseq	-0.223	0.14
low_pH_jason_reseq	-0.714	-1.631
NO_jason_reseq	0.071	-0.32
B6_jason_reseq	0.016	0.24
MHCII_jason_reseq	0.209	0.762
Isoniazid02	-0.113	-0.473
Rifampicin4	-0.097	0.671
Ethambutol3	-0.022	-0.406
Meropenem3	-0.4	0.059
Vancomycin16	-0.194	-0.194
Rv2680_day32	-1.068	0.061
H37Rv_KO_MarP	-0.078	-0.045
hypoxia_3wks	0.171	-0.175
hypoxia_6wks	0.177	-0.76
glycerol	-0.658	0.581
cholesterol	-0.495	0.441
AJ	-0.126	0.197
Bibs02	-0.099	0.228
Bibs02c	0.391	0.782
BL6	0.237	0.332
BL6a	0.194	0.74
BXD01	0.109	0.276
BXD010	0.549	-0.058
BXD011	0.467	-0.107
BXD03	0.122	0.133
BXD04	0.014	-0.047
BXD05	-0.453	0.468
BXD06	0.035	-0.06
BXD07	0.259	0.117
BXD08	0.491	0.412
BXD09	0.253	0.148
CAST	0.272	0.637
CCcont	0.236	0.106
DS01	0.062	-0.161
DS02	-0.076	0.17
DS04	0.169	0.447
DS0c	0.314	-0.218
GP01	0.099	0.25
GP02	0.592	0.146
GP0c	-0.056	-0.039
NOD	0.234	0.236
NZO	0.513	-0.201
PWK	0.428	-0.104
H37Rv_KO_CtpC	0.364	0.265
H37Rv_KO_CtpD	0.696	0.351
H37Rv_KO_Rv1272	1.149	0.952
H37Rv_KO_SugABC	0.374	0.895
H37Rv_KO_MbtN	0.381	0.369
Trans05	0.325	0.419
macrophage_unactivated	0.139	1.004
IL1	0.332	0.225
Rapamycin	0.04	0.847
Tcell	0.029	0.534
GMCSF	0.174	0.069
IFNab	0.121	0.378
IFNg	0.484	0.313
IFNg_GMCSF1	0.531	0.214
Rv1432_day32	0.519	0.272
Rv1565c_day32	0.21	-0.351
secA2_input	0.913	0.094
delta_Rv3594	0.095	-0.162
delta_Rv3717	-0.249	-0.646
delta_Rv3811	-0.397	-0.47
delta_Rv0954	-0.649	-0.885
PonA1	-0.321	-0.247
EccD1_KO	0.227	0.02
EspI_KO	0.465	-0.128
PE35_KO	0.376	-0.248
PPE68_KO	0.118	-0.294
glycerol2	0.738	1.338
lignocerate	0.82	1.169
oleate	1.007	1.262
phosphatidylcholine	0.91	1.195
acetate	0.096	0.281
glucAc	0.207	0.554
Rv0950ko	0.874	0.208
Rv1096ko	0.214	0.208
Rv3684ko	0.049	0.226
delta_otsA_trehalose	0.871	-0.152