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 Rv1564c/treX:

update plot	correlation	link to info on gene
Rv3363c/-	(cc=0.5751)	info on Rv3363c/-
Rv3168/-	(cc=0.5383)	info on Rv3168/-
Rv3218/-	(cc=0.479)	info on Rv3218/-
Rv0045c/-	(cc=0.4724)	info on Rv0045c/-
Rv1513/-	(cc=0.4578)	info on Rv1513/-
Rv2655c/-	(cc=0.4573)	info on Rv2655c/-
Rv0551c/fadD8	(cc=0.457)	info on Rv0551c/fadD8
Rv3320c/vapC44	(cc=0.4508)	info on Rv3320c/vapC44
Rv0592/mce2D	(cc=0.4396)	info on Rv0592/mce2D
Rv0112/gca	(cc=0.4356)	info on Rv0112/gca

Correlation of Rv1564c/treX with Rv0551c/fadD8

Normalized LFCs for Rv1564c/treX:
(description and provenance of datasets)

	Rv1564c/treX	Rv0551c/fadD8
Fe_supp_jason_reseq	0.115	-0.404
low_pH_jason_reseq	0.877	-0.704
NO_jason_reseq	0.617	0.417
B6_jason_reseq	1.042	0.214
MHCII_jason_reseq	0.449	0.397
Isoniazid02	0.048	-0.506
Rifampicin4	0.845	-0.441
Ethambutol3	0.395	-0.303
Meropenem3	1.053	0.243
Vancomycin16	0.417	0.0
Rv2680_day32	0.667	0.37
H37Rv_KO_MarP	0.742	0.202
hypoxia_3wks	1.902	0.502
hypoxia_6wks	0.647	0.798
glycerol	-0.344	-0.097
cholesterol	-0.247	-0.025
AJ	0.166	0.615
Bibs02	0.409	0.258
Bibs02c	-0.039	-0.23
BL6	0.985	-0.17
BL6a	0.29	-0.106
BXD01	0.412	0.116
BXD010	0.482	0.219
BXD011	0.463	0.249
BXD03	0.544	0.091
BXD04	0.357	0.07
BXD05	0.607	0.098
BXD06	0.658	0.395
BXD07	0.931	0.416
BXD08	0.226	0.329
BXD09	0.356	0.288
CAST	0.697	0.217
CCcont	-0.028	-0.285
DS01	-0.852	0.272
DS02	-0.517	0.403
DS04	-0.885	0.777
DS0c	-0.841	0.536
GP01	0.969	0.765
GP02	0.217	-0.081
GP0c	0.464	0.122
NOD	-0.241	0.212
NZO	0.851	-0.035
PWK	1.611	0.277
H37Rv_KO_CtpC	-0.586	-0.067
H37Rv_KO_CtpD	-0.346	-0.351
H37Rv_KO_Rv1272	-0.319	-0.016
H37Rv_KO_SugABC	0.293	-0.023
H37Rv_KO_MbtN	1.052	-0.385
Trans05	0.222	-0.844
macrophage_unactivated	0.0	0.256
IL1	0.258	-0.151
Rapamycin	-0.08	-0.344
Tcell	-0.085	-0.515
GMCSF	0.0	-0.135
IFNab	-0.039	-0.447
IFNg	0.102	-0.422
IFNg_GMCSF1	0.352	-0.613
Rv1432_day32	0.997	-0.241
Rv1565c_day32	0.103	0.569
secA2_input	-0.753	0.667
delta_Rv3594	-0.621	0.476
delta_Rv3717	0.17	0.547
delta_Rv3811	-0.631	-0.23
delta_Rv0954	-0.255	0.43
PonA1	-0.557	0.716
EccD1_KO	-1.503	-0.109
EspI_KO	-1.101	-0.422
PE35_KO	-0.379	0.0
PPE68_KO	-0.806	-0.362
glycerol2	-0.926	-0.098
lignocerate	-0.788	-0.151
oleate	-0.917	0.162
phosphatidylcholine	-0.711	0.043
acetate	-0.404	-0.419
glucAc	-0.206	-0.664
Rv0950ko	-0.112	0.0
Rv1096ko	-0.29	0.495
Rv3684ko	-0.445	0.239
delta_otsA_trehalose	3.876	4.154