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 Rv3475/-:

update plot	correlation	link to info on gene
Rv2649/-	(cc=0.9737)	info on Rv2649/-
Rv3185/-	(cc=0.9674)	info on Rv3185/-
Rv1369c/-	(cc=0.9666)	info on Rv1369c/-
Rv3326/-	(cc=0.9661)	info on Rv3326/-
Rv1764/-	(cc=0.9637)	info on Rv1764/-
Rv1756c/-	(cc=0.963)	info on Rv1756c/-
Rv2814c/-	(cc=0.9629)	info on Rv2814c/-
Rv2167c/-	(cc=0.9561)	info on Rv2167c/-
Rv0796/-	(cc=0.9558)	info on Rv0796/-
Rv2279/-	(cc=0.955)	info on Rv2279/-

Correlation of Rv3475/- with Rv2279/-

Normalized LFCs for Rv3475/-:
(description and provenance of datasets)

	Rv3475/-	Rv2279/-
Fe_supp_jason_reseq	-0.456	-0.382
low_pH_jason_reseq	-0.413	-0.641
NO_jason_reseq	0.179	0.108
B6_jason_reseq	-0.671	-0.639
MHCII_jason_reseq	-0.15	-0.25
Isoniazid02	0.0	-0.192
Rifampicin4	0.942	0.726
Ethambutol3	0.591	0.392
Meropenem3	-0.201	-0.368
Vancomycin16	0.117	-0.212
Rv2680_day32	0.249	0.346
H37Rv_KO_MarP	-0.253	-0.233
hypoxia_3wks	0.439	0.478
hypoxia_6wks	0.161	-0.077
glycerol	-0.549	-0.712
cholesterol	0.198	0.118
AJ	1.348	1.329
Bibs02	1.098	1.094
Bibs02c	1.491	1.557
BL6	0.014	0.329
BL6a	0.897	1.135
BXD01	0.73	0.672
BXD010	0.761	0.917
BXD011	0.827	0.842
BXD03	0.847	0.77
BXD04	0.477	0.549
BXD05	1.002	1.112
BXD06	0.547	0.542
BXD07	0.881	0.885
BXD08	0.53	0.408
BXD09	0.673	0.809
CAST	1.17	1.211
CCcont	-0.026	0.121
DS01	0.922	0.58
DS02	0.934	0.666
DS04	1.107	0.939
DS0c	1.039	0.831
GP01	1.169	1.016
GP02	1.477	1.219
GP0c	0.835	0.509
NOD	1.334	1.087
NZO	1.006	1.181
PWK	1.216	1.218
H37Rv_KO_CtpC	0.741	0.792
H37Rv_KO_CtpD	0.814	0.692
H37Rv_KO_Rv1272	0.492	0.414
H37Rv_KO_SugABC	0.875	0.925
H37Rv_KO_MbtN	0.553	0.535
Trans05	0.771	0.782
macrophage_unactivated	-0.95	-0.739
IL1	-0.217	-0.276
Rapamycin	-0.638	-0.427
Tcell	-0.981	-1.456
GMCSF	-0.103	-0.129
IFNab	-0.674	-0.774
IFNg	-0.42	-0.299
IFNg_GMCSF1	-0.295	-0.116
Rv1432_day32	0.837	0.557
Rv1565c_day32	0.167	0.104
secA2_input	0.072	0.0
delta_Rv3594	-0.066	-0.026
delta_Rv3717	-0.109	-0.237
delta_Rv3811	-0.156	-0.128
delta_Rv0954	0.41	0.485
PonA1	0.122	-0.02
EccD1_KO	0.155	-0.224
EspI_KO	1.184	1.055
PE35_KO	1.05	0.583
PPE68_KO	0.819	0.253
glycerol2	-0.771	-0.657
lignocerate	-0.728	-0.279
oleate	-0.767	-0.934
phosphatidylcholine	-0.718	-0.585
acetate	0.0	0.158
glucAc	-0.168	0.244
Rv0950ko	-0.178	-0.021
Rv1096ko	0.057	-0.13
Rv3684ko	-0.783	-0.534
delta_otsA_trehalose	0.549	0.281