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 Rv3326/-

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

	Rv3475/-	Rv3326/-
Fe_supp_jason_reseq	-0.456	-0.294
low_pH_jason_reseq	-0.413	-0.495
NO_jason_reseq	0.179	0.265
B6_jason_reseq	-0.671	-0.452
MHCII_jason_reseq	-0.15	0.006
Isoniazid02	0.0	-0.137
Rifampicin4	0.942	0.977
Ethambutol3	0.591	0.362
Meropenem3	-0.201	-0.406
Vancomycin16	0.117	-0.106
Rv2680_day32	0.249	0.284
H37Rv_KO_MarP	-0.253	-0.253
hypoxia_3wks	0.439	0.506
hypoxia_6wks	0.161	0.223
glycerol	-0.549	-0.892
cholesterol	0.198	-0.03
AJ	1.348	1.237
Bibs02	1.098	1.121
Bibs02c	1.491	1.554
BL6	0.014	0.044
BL6a	0.897	1.116
BXD01	0.73	0.757
BXD010	0.761	0.918
BXD011	0.827	0.89
BXD03	0.847	0.818
BXD04	0.477	0.526
BXD05	1.002	1.101
BXD06	0.547	0.644
BXD07	0.881	0.861
BXD08	0.53	0.672
BXD09	0.673	0.833
CAST	1.17	1.256
CCcont	-0.026	0.0
DS01	0.922	1.013
DS02	0.934	0.803
DS04	1.107	1.138
DS0c	1.039	1.101
GP01	1.169	1.272
GP02	1.477	1.291
GP0c	0.835	0.656
NOD	1.334	1.447
NZO	1.006	0.922
PWK	1.216	1.196
H37Rv_KO_CtpC	0.741	0.757
H37Rv_KO_CtpD	0.814	0.812
H37Rv_KO_Rv1272	0.492	0.393
H37Rv_KO_SugABC	0.875	0.851
H37Rv_KO_MbtN	0.553	0.517
Trans05	0.771	0.728
macrophage_unactivated	-0.95	-0.846
IL1	-0.217	-0.572
Rapamycin	-0.638	-0.865
Tcell	-0.981	-1.505
GMCSF	-0.103	-0.438
IFNab	-0.674	-0.937
IFNg	-0.42	-0.66
IFNg_GMCSF1	-0.295	-0.544
Rv1432_day32	0.837	0.405
Rv1565c_day32	0.167	0.387
secA2_input	0.072	0.0
delta_Rv3594	-0.066	-0.13
delta_Rv3717	-0.109	-0.198
delta_Rv3811	-0.156	-0.126
delta_Rv0954	0.41	0.581
PonA1	0.122	-0.02
EccD1_KO	0.155	0.24
EspI_KO	1.184	0.99
PE35_KO	1.05	1.254
PPE68_KO	0.819	0.761
glycerol2	-0.771	-0.757
lignocerate	-0.728	-0.578
oleate	-0.767	-0.89
phosphatidylcholine	-0.718	-0.69
acetate	0.0	0.032
glucAc	-0.168	0.123
Rv0950ko	-0.178	0.145
Rv1096ko	0.057	0.021
Rv3684ko	-0.783	-0.21
delta_otsA_trehalose	0.549	0.274