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 Rv0778/cyp126:

update plot	correlation	link to info on gene
Rv0892/-	(cc=0.5985)	info on Rv0892/-
Rv0766c/cyp123	(cc=0.4897)	info on Rv0766c/cyp123
Rv0003/recF	(cc=0.486)	info on Rv0003/recF
Rv2537c/aroD	(cc=0.4777)	info on Rv2537c/aroD
Rv3116/moeB2	(cc=0.4552)	info on Rv3116/moeB2
Rv2530c/vapC39	(cc=0.4494)	info on Rv2530c/vapC39
Rv1298/rpmE	(cc=0.4475)	info on Rv1298/rpmE
Rv0781/ptrBa	(cc=0.4441)	info on Rv0781/ptrBa
Rv3104c/-	(cc=0.4422)	info on Rv3104c/-
Rv3125c/PPE49	(cc=0.4272)	info on Rv3125c/PPE49

Correlation of Rv0778/cyp126 with Rv3116/moeB2

Normalized LFCs for Rv0778/cyp126:
(description and provenance of datasets)

	Rv0778/cyp126	Rv3116/moeB2
Fe_supp_jason_reseq	2.014	0.753
low_pH_jason_reseq	-0.571	-0.539
NO_jason_reseq	-0.651	-0.483
B6_jason_reseq	0.523	0.435
MHCII_jason_reseq	0.706	0.474
Isoniazid02	-0.525	-1.141
Rifampicin4	0.157	-0.051
Ethambutol3	-0.403	-0.544
Meropenem3	0.298	-1.06
Vancomycin16	0.154	-0.332
Rv2680_day32	0.508	-0.749
H37Rv_KO_MarP	-0.423	-0.322
hypoxia_3wks	0.534	0.279
hypoxia_6wks	-0.021	-0.184
glycerol	0.736	-0.707
cholesterol	0.449	-0.491
AJ	0.824	-0.235
Bibs02	0.174	-0.445
Bibs02c	0.246	0.099
BL6	-0.148	0.681
BL6a	0.756	0.763
BXD01	0.734	0.64
BXD010	0.959	0.848
BXD011	0.899	1.007
BXD03	0.561	0.782
BXD04	1.184	0.983
BXD05	0.862	1.152
BXD06	0.836	0.642
BXD07	0.79	0.666
BXD08	0.618	0.673
BXD09	0.696	0.712
CAST	0.756	-0.057
CCcont	-0.056	0.584
DS01	0.921	0.435
DS02	1.078	0.777
DS04	0.207	0.555
DS0c	0.919	0.383
GP01	-0.265	0.277
GP02	-0.021	0.652
GP0c	0.665	0.307
NOD	1.642	-0.111
NZO	0.581	-0.256
PWK	0.715	-0.287
H37Rv_KO_CtpC	0.916	0.608
H37Rv_KO_CtpD	1.194	0.987
H37Rv_KO_Rv1272	-0.269	0.52
H37Rv_KO_SugABC	1.345	0.234
H37Rv_KO_MbtN	0.918	0.791
Trans05	0.278	0.687
macrophage_unactivated	1.042	0.275
IL1	0.0	-0.133
Rapamycin	0.341	-0.356
Tcell	0.437	0.094
GMCSF	0.591	0.391
IFNab	0.0	-0.16
IFNg	1.04	-0.374
IFNg_GMCSF1	0.566	0.091
Rv1432_day32	-0.624	-0.168
Rv1565c_day32	-0.347	-0.158
secA2_input	0.23	-0.704
delta_Rv3594	0.72	0.265
delta_Rv3717	-0.162	0.036
delta_Rv3811	0.744	-0.18
delta_Rv0954	0.549	0.224
PonA1	0.753	0.066
EccD1_KO	0.52	-0.22
EspI_KO	0.893	-0.026
PE35_KO	0.983	-0.222
PPE68_KO	0.841	-0.029
glycerol2	-0.13	0.252
lignocerate	-0.614	-0.142
oleate	0.39	0.885
phosphatidylcholine	0.088	0.293
acetate	-0.748	-0.61
glucAc	-1.202	-1.047
Rv0950ko	0.329	-0.072
Rv1096ko	0.633	-0.977
Rv3684ko	0.121	-0.603
delta_otsA_trehalose	-1.184	-0.223