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 Rv3749c/-:

update plot	correlation	link to info on gene
Rv2287/yjcE	(cc=0.8532)	info on Rv2287/yjcE
Rv1913/-	(cc=0.8224)	info on Rv1913/-
Rv0293c/-	(cc=0.7675)	info on Rv0293c/-
Rv1356c/-	(cc=0.7432)	info on Rv1356c/-
Rv0182c/sigG	(cc=0.7014)	info on Rv0182c/sigG
Rv3812/PE_PGRS62	(cc=0.6826)	info on Rv3812/PE_PGRS62
Rv2668/-	(cc=0.6646)	info on Rv2668/-
Rv0187/-	(cc=0.6288)	info on Rv0187/-
Rv3697c/vapC48	(cc=0.6188)	info on Rv3697c/vapC48
Rv1366/-	(cc=0.6056)	info on Rv1366/-

Correlation of Rv3749c/- with Rv1366/-

Normalized LFCs for Rv3749c/-:
(description and provenance of datasets)

	Rv3749c/-	Rv1366/-
Fe_supp_jason_reseq	0.253	-0.884
low_pH_jason_reseq	-0.602	-0.172
NO_jason_reseq	0.026	-0.294
B6_jason_reseq	0.466	-0.871
MHCII_jason_reseq	0.688	-0.267
Isoniazid02	-0.227	0.148
Rifampicin4	0.062	-0.376
Ethambutol3	0.136	0.269
Meropenem3	-0.904	0.237
Vancomycin16	-0.464	0.172
Rv2680_day32	-0.008	-0.969
H37Rv_KO_MarP	0.429	0.518
hypoxia_3wks	-0.1	-0.235
hypoxia_6wks	-0.098	-0.048
glycerol	-2.336	-0.78
cholesterol	-1.456	-0.44
AJ	0.225	0.134
Bibs02	-0.535	-0.823
Bibs02c	0.779	0.656
BL6	-0.411	0.376
BL6a	0.532	0.397
BXD01	-0.171	0.834
BXD010	0.558	1.115
BXD011	-0.294	0.35
BXD03	-0.054	-0.278
BXD04	-0.348	0.315
BXD05	0.359	0.231
BXD06	-0.489	0.323
BXD07	-0.021	0.476
BXD08	-0.206	0.506
BXD09	-0.101	-0.012
CAST	0.354	-0.142
CCcont	-0.373	0.646
DS01	-0.101	0.301
DS02	-0.487	-0.254
DS04	-0.521	0.263
DS0c	0.193	0.525
GP01	1.065	1.227
GP02	-0.271	1.296
GP0c	-0.257	0.54
NOD	0.716	0.148
NZO	0.077	0.839
PWK	0.175	0.406
H37Rv_KO_CtpC	-0.755	0.467
H37Rv_KO_CtpD	-0.643	-0.907
H37Rv_KO_Rv1272	-0.229	0.341
H37Rv_KO_SugABC	-0.009	0.902
H37Rv_KO_MbtN	-1.433	0.392
Trans05	-0.542	0.557
macrophage_unactivated	-1.386	0.107
IL1	-5.09	-0.739
Rapamycin	-4.944	-0.681
Tcell	2.366	0.694
GMCSF	-4.267	-1.117
IFNab	-4.734	-0.593
IFNg	-4.479	-1.384
IFNg_GMCSF1	-5.144	-1.628
Rv1432_day32	0.077	-0.55
Rv1565c_day32	0.18	0.175
secA2_input	-0.941	-0.188
delta_Rv3594	-0.393	-0.249
delta_Rv3717	-0.339	0.371
delta_Rv3811	-0.082	-0.665
delta_Rv0954	0.141	0.813
PonA1	-0.029	0.726
EccD1_KO	-0.428	-0.276
EspI_KO	-0.034	0.262
PE35_KO	-0.604	0.379
PPE68_KO	-0.877	0.534
glycerol2	0.901	1.188
lignocerate	0.793	1.47
oleate	0.906	0.387
phosphatidylcholine	1.018	1.27
acetate	0.318	1.549
glucAc	0.22	1.226
Rv0950ko	0.356	0.856
Rv1096ko	0.425	0.32
Rv3684ko	-0.016	0.534
delta_otsA_trehalose	1.092	1.077