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 Rv2530c/vapC39

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

	Rv0778/cyp126	Rv2530c/vapC39
Fe_supp_jason_reseq	2.014	2.021
low_pH_jason_reseq	-0.571	1.586
NO_jason_reseq	-0.651	-0.281
B6_jason_reseq	0.523	-0.538
MHCII_jason_reseq	0.706	-0.217
Isoniazid02	-0.525	0.546
Rifampicin4	0.157	0.474
Ethambutol3	-0.403	-0.089
Meropenem3	0.298	-0.053
Vancomycin16	0.154	1.305
Rv2680_day32	0.508	1.701
H37Rv_KO_MarP	-0.423	-0.165
hypoxia_3wks	0.534	0.187
hypoxia_6wks	-0.021	-0.228
glycerol	0.736	1.463
cholesterol	0.449	0.0
AJ	0.824	0.0
Bibs02	0.174	0.0
Bibs02c	0.246	0.0
BL6	-0.148	0.0
BL6a	0.756	3.566
BXD01	0.734	3.731
BXD010	0.959	3.969
BXD011	0.899	2.955
BXD03	0.561	1.849
BXD04	1.184	2.75
BXD05	0.862	3.385
BXD06	0.836	3.49
BXD07	0.79	3.809
BXD08	0.618	2.491
BXD09	0.696	3.016
CAST	0.756	0.23
CCcont	-0.056	0.285
DS01	0.921	0.0
DS02	1.078	0.0
DS04	0.207	0.533
DS0c	0.919	0.0
GP01	-0.265	1.43
GP02	-0.021	2.139
GP0c	0.665	3.221
NOD	1.642	0.225
NZO	0.581	0.0
PWK	0.715	0.0
H37Rv_KO_CtpC	0.916	4.288
H37Rv_KO_CtpD	1.194	5.372
H37Rv_KO_Rv1272	-0.269	0.495
H37Rv_KO_SugABC	1.345	0.272
H37Rv_KO_MbtN	0.918	0.437
Trans05	0.278	4.469
macrophage_unactivated	1.042	2.5
IL1	0.0	0.492
Rapamycin	0.341	0.411
Tcell	0.437	2.9
GMCSF	0.591	-1.735
IFNab	0.0	1.587
IFNg	1.04	-0.294
IFNg_GMCSF1	0.566	3.086
Rv1432_day32	-0.624	0.0
Rv1565c_day32	-0.347	0.218
secA2_input	0.23	0.294
delta_Rv3594	0.72	1.667
delta_Rv3717	-0.162	0.635
delta_Rv3811	0.744	2.214
delta_Rv0954	0.549	1.858
PonA1	0.753	3.233
EccD1_KO	0.52	-2.684
EspI_KO	0.893	1.241
PE35_KO	0.983	0.823
PPE68_KO	0.841	-0.106
glycerol2	-0.13	-0.42
lignocerate	-0.614	-1.112
oleate	0.39	1.036
phosphatidylcholine	0.088	0.366
acetate	-0.748	-1.44
glucAc	-1.202	-3.978
Rv0950ko	0.329	0.691
Rv1096ko	0.633	0.513
Rv3684ko	0.121	-0.305
delta_otsA_trehalose	-1.184	-0.503