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 Rv2649/-

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

	Rv3475/-	Rv2649/-
Fe_supp_jason_reseq	-0.456	-0.259
low_pH_jason_reseq	-0.413	-0.333
NO_jason_reseq	0.179	0.236
B6_jason_reseq	-0.671	-0.422
MHCII_jason_reseq	-0.15	0.0
Isoniazid02	0.0	0.057
Rifampicin4	0.942	1.075
Ethambutol3	0.591	0.612
Meropenem3	-0.201	-0.132
Vancomycin16	0.117	0.088
Rv2680_day32	0.249	0.169
H37Rv_KO_MarP	-0.253	-0.157
hypoxia_3wks	0.439	0.431
hypoxia_6wks	0.161	0.077
glycerol	-0.549	-0.635
cholesterol	0.198	0.144
AJ	1.348	1.351
Bibs02	1.098	1.125
Bibs02c	1.491	1.814
BL6	0.014	0.029
BL6a	0.897	0.911
BXD01	0.73	0.613
BXD010	0.761	0.729
BXD011	0.827	0.75
BXD03	0.847	0.661
BXD04	0.477	0.473
BXD05	1.002	0.959
BXD06	0.547	0.423
BXD07	0.881	0.702
BXD08	0.53	0.433
BXD09	0.673	0.667
CAST	1.17	1.303
CCcont	-0.026	0.009
DS01	0.922	1.042
DS02	0.934	0.901
DS04	1.107	1.143
DS0c	1.039	1.122
GP01	1.169	1.149
GP02	1.477	1.403
GP0c	0.835	0.705
NOD	1.334	1.256
NZO	1.006	1.019
PWK	1.216	1.162
H37Rv_KO_CtpC	0.741	0.771
H37Rv_KO_CtpD	0.814	0.903
H37Rv_KO_Rv1272	0.492	0.47
H37Rv_KO_SugABC	0.875	0.757
H37Rv_KO_MbtN	0.553	0.647
Trans05	0.771	0.804
macrophage_unactivated	-0.95	-0.865
IL1	-0.217	-0.365
Rapamycin	-0.638	-0.466
Tcell	-0.981	-1.268
GMCSF	-0.103	-0.269
IFNab	-0.674	-0.707
IFNg	-0.42	-0.347
IFNg_GMCSF1	-0.295	-0.148
Rv1432_day32	0.837	0.533
Rv1565c_day32	0.167	0.13
secA2_input	0.072	-0.337
delta_Rv3594	-0.066	-0.121
delta_Rv3717	-0.109	-0.111
delta_Rv3811	-0.156	-0.064
delta_Rv0954	0.41	0.457
PonA1	0.122	0.0
EccD1_KO	0.155	0.099
EspI_KO	1.184	0.858
PE35_KO	1.05	0.75
PPE68_KO	0.819	0.33
glycerol2	-0.771	-0.954
lignocerate	-0.728	-0.756
oleate	-0.767	-1.069
phosphatidylcholine	-0.718	-0.828
acetate	0.0	-0.329
glucAc	-0.168	-0.013
Rv0950ko	-0.178	-0.148
Rv1096ko	0.057	0.06
Rv3684ko	-0.783	-0.599
delta_otsA_trehalose	0.549	0.193