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 Rv2537c/aroD

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

	Rv0778/cyp126	Rv2537c/aroD
Fe_supp_jason_reseq	2.014	1.148
low_pH_jason_reseq	-0.571	-1.29
NO_jason_reseq	-0.651	0.0
B6_jason_reseq	0.523	-1.704
MHCII_jason_reseq	0.706	-1.501
Isoniazid02	-0.525	-0.167
Rifampicin4	0.157	-0.311
Ethambutol3	-0.403	-0.14
Meropenem3	0.298	-0.138
Vancomycin16	0.154	0.0
Rv2680_day32	0.508	0.0
H37Rv_KO_MarP	-0.423	-1.662
hypoxia_3wks	0.534	0.459
hypoxia_6wks	-0.021	0.464
glycerol	0.736	-0.385
cholesterol	0.449	-0.276
AJ	0.824	0.193
Bibs02	0.174	-0.348
Bibs02c	0.246	-0.399
BL6	-0.148	-0.238
BL6a	0.756	0.595
BXD01	0.734	0.695
BXD010	0.959	0.0
BXD011	0.899	0.0
BXD03	0.561	0.856
BXD04	1.184	0.524
BXD05	0.862	-0.123
BXD06	0.836	0.566
BXD07	0.79	0.809
BXD08	0.618	1.127
BXD09	0.696	0.675
CAST	0.756	-0.439
CCcont	-0.056	-0.285
DS01	0.921	-0.45
DS02	1.078	-0.414
DS04	0.207	0.0
DS0c	0.919	-0.413
GP01	-0.265	-0.188
GP02	-0.021	-0.159
GP0c	0.665	-0.248
NOD	1.642	-0.428
NZO	0.581	-0.38
PWK	0.715	-0.374
H37Rv_KO_CtpC	0.916	0.0
H37Rv_KO_CtpD	1.194	1.56
H37Rv_KO_Rv1272	-0.269	-0.269
H37Rv_KO_SugABC	1.345	3.352
H37Rv_KO_MbtN	0.918	-0.094
Trans05	0.278	0.698
macrophage_unactivated	1.042	0.0
IL1	0.0	0.0
Rapamycin	0.341	1.068
Tcell	0.437	0.209
GMCSF	0.591	-0.177
IFNab	0.0	0.0
IFNg	1.04	-0.369
IFNg_GMCSF1	0.566	0.0
Rv1432_day32	-0.624	-1.55
Rv1565c_day32	-0.347	0.0
secA2_input	0.23	0.628
delta_Rv3594	0.72	-1.071
delta_Rv3717	-0.162	0.378
delta_Rv3811	0.744	-0.564
delta_Rv0954	0.549	-0.398
PonA1	0.753	-1.154
EccD1_KO	0.52	1.23
EspI_KO	0.893	1.298
PE35_KO	0.983	0.971
PPE68_KO	0.841	0.486
glycerol2	-0.13	-2.27
lignocerate	-0.614	-2.59
oleate	0.39	-0.997
phosphatidylcholine	0.088	-1.804
acetate	-0.748	-2.003
glucAc	-1.202	-3.156
Rv0950ko	0.329	0.247
Rv1096ko	0.633	0.0
Rv3684ko	0.121	-0.593
delta_otsA_trehalose	-1.184	0.544