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 Rv0781/ptrBa

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

	Rv0778/cyp126	Rv0781/ptrBa
Fe_supp_jason_reseq	2.014	-0.268
low_pH_jason_reseq	-0.571	0.0
NO_jason_reseq	-0.651	-0.291
B6_jason_reseq	0.523	0.921
MHCII_jason_reseq	0.706	0.84
Isoniazid02	-0.525	0.0
Rifampicin4	0.157	0.236
Ethambutol3	-0.403	-0.113
Meropenem3	0.298	-0.231
Vancomycin16	0.154	0.451
Rv2680_day32	0.508	0.855
H37Rv_KO_MarP	-0.423	0.865
hypoxia_3wks	0.534	0.558
hypoxia_6wks	-0.021	-0.257
glycerol	0.736	-0.584
cholesterol	0.449	0.24
AJ	0.824	0.524
Bibs02	0.174	0.413
Bibs02c	0.246	-0.706
BL6	-0.148	1.035
BL6a	0.756	1.128
BXD01	0.734	1.199
BXD010	0.959	0.588
BXD011	0.899	1.902
BXD03	0.561	0.852
BXD04	1.184	1.888
BXD05	0.862	0.794
BXD06	0.836	1.014
BXD07	0.79	1.355
BXD08	0.618	1.321
BXD09	0.696	1.663
CAST	0.756	0.651
CCcont	-0.056	1.082
DS01	0.921	-0.27
DS02	1.078	-0.629
DS04	0.207	-0.967
DS0c	0.919	0.786
GP01	-0.265	-1.099
GP02	-0.021	-0.843
GP0c	0.665	-1.091
NOD	1.642	0.441
NZO	0.581	1.296
PWK	0.715	1.623
H37Rv_KO_CtpC	0.916	-0.06
H37Rv_KO_CtpD	1.194	1.006
H37Rv_KO_Rv1272	-0.269	-0.219
H37Rv_KO_SugABC	1.345	0.681
H37Rv_KO_MbtN	0.918	-0.865
Trans05	0.278	-0.812
macrophage_unactivated	1.042	1.521
IL1	0.0	-0.163
Rapamycin	0.341	-0.439
Tcell	0.437	-0.274
GMCSF	0.591	0.14
IFNab	0.0	-0.432
IFNg	1.04	-0.072
IFNg_GMCSF1	0.566	0.0
Rv1432_day32	-0.624	0.445
Rv1565c_day32	-0.347	-0.199
secA2_input	0.23	-1.263
delta_Rv3594	0.72	0.702
delta_Rv3717	-0.162	0.81
delta_Rv3811	0.744	1.276
delta_Rv0954	0.549	0.506
PonA1	0.753	0.0
EccD1_KO	0.52	-0.171
EspI_KO	0.893	0.676
PE35_KO	0.983	0.0
PPE68_KO	0.841	0.0
glycerol2	-0.13	-2.413
lignocerate	-0.614	-2.233
oleate	0.39	-2.633
phosphatidylcholine	0.088	-2.323
acetate	-0.748	-2.592
glucAc	-1.202	-0.911
Rv0950ko	0.329	0.458
Rv1096ko	0.633	0.347
Rv3684ko	0.121	0.498
delta_otsA_trehalose	-1.184	-1.892