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 Rv0425c/ctpH:

update plot	correlation	link to info on gene
Rv0644c/mmaA2	(cc=0.7169)	info on Rv0644c/mmaA2
Rv1780/-	(cc=0.7118)	info on Rv1780/-
Rv0645c/mmaA1	(cc=0.7049)	info on Rv0645c/mmaA1
Rv3050c/-	(cc=0.6845)	info on Rv3050c/-
Rv0502/-	(cc=0.6675)	info on Rv0502/-
Rv2185c/TB16.3	(cc=0.6456)	info on Rv2185c/TB16.3
Rv0642c/mmaA4	(cc=0.6388)	info on Rv0642c/mmaA4
Rv0473/-	(cc=0.6308)	info on Rv0473/-
Rv1925/fadD31	(cc=0.6203)	info on Rv1925/fadD31
Rv0183/-	(cc=0.6124)	info on Rv0183/-

Correlation of Rv0425c/ctpH with Rv0645c/mmaA1

Normalized LFCs for Rv0425c/ctpH:
(description and provenance of datasets)

	Rv0425c/ctpH	Rv0645c/mmaA1
Fe_supp_jason_reseq	-1.718	0.107
low_pH_jason_reseq	1.173	0.637
NO_jason_reseq	0.118	0.995
B6_jason_reseq	-0.236	2.126
MHCII_jason_reseq	-0.013	1.105
Isoniazid02	-0.111	0.914
Rifampicin4	0.701	-1.389
Ethambutol3	-0.581	-0.306
Meropenem3	-0.163	0.21
Vancomycin16	-0.255	-1.273
Rv2680_day32	2.133	2.853
H37Rv_KO_MarP	0.419	0.066
hypoxia_3wks	1.037	0.49
hypoxia_6wks	1.599	2.583
glycerol	0.743	-0.214
cholesterol	0.278	-0.666
AJ	0.151	-0.064
Bibs02	0.734	-0.715
Bibs02c	0.264	-0.167
BL6	0.794	1.596
BL6a	1.347	1.415
BXD01	1.183	2.284
BXD010	1.184	2.033
BXD011	1.811	3.383
BXD03	0.677	1.125
BXD04	1.388	1.855
BXD05	1.185	1.878
BXD06	1.52	2.018
BXD07	0.914	2.279
BXD08	1.311	2.369
BXD09	1.391	2.252
CAST	-0.357	1.013
CCcont	0.251	0.102
DS01	0.491	-0.44
DS02	0.726	0.296
DS04	0.675	-0.159
DS0c	0.486	-0.822
GP01	1.245	2.116
GP02	1.46	2.451
GP0c	0.667	1.458
NOD	-0.226	0.195
NZO	0.552	1.079
PWK	-0.097	0.189
H37Rv_KO_CtpC	0.178	0.047
H37Rv_KO_CtpD	-1.43	0.307
H37Rv_KO_Rv1272	1.055	0.635
H37Rv_KO_SugABC	0.736	1.228
H37Rv_KO_MbtN	1.73	1.404
Trans05	2.05	1.652
macrophage_unactivated	-0.41	-0.928
IL1	0.997	0.457
Rapamycin	0.755	-0.405
Tcell	2.108	0.613
GMCSF	0.119	0.066
IFNab	-0.502	-0.665
IFNg	0.254	0.684
IFNg_GMCSF1	0.041	1.119
Rv1432_day32	3.046	5.021
Rv1565c_day32	-0.291	-0.164
secA2_input	0.326	0.194
delta_Rv3594	-0.081	0.736
delta_Rv3717	2.065	2.551
delta_Rv3811	0.813	1.344
delta_Rv0954	-1.301	-0.438
PonA1	-0.862	-0.88
EccD1_KO	-1.812	-0.799
EspI_KO	-2.139	-0.665
PE35_KO	-1.779	-1.24
PPE68_KO	-1.718	-1.206
glycerol2	0.27	0.581
lignocerate	0.726	0.11
oleate	-0.403	0.006
phosphatidylcholine	0.249	0.347
acetate	0.733	0.027
glucAc	0.628	0.549
Rv0950ko	-0.826	0.404
Rv1096ko	-0.591	-0.29
Rv3684ko	-0.085	0.501
delta_otsA_trehalose	-0.203	0.573