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 Rv3104c/-

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

	Rv0778/cyp126	Rv3104c/-
Fe_supp_jason_reseq	2.014	1.44
low_pH_jason_reseq	-0.571	-0.574
NO_jason_reseq	-0.651	-0.704
B6_jason_reseq	0.523	-0.434
MHCII_jason_reseq	0.706	0.884
Isoniazid02	-0.525	0.127
Rifampicin4	0.157	0.192
Ethambutol3	-0.403	-0.592
Meropenem3	0.298	0.458
Vancomycin16	0.154	-0.175
Rv2680_day32	0.508	-0.354
H37Rv_KO_MarP	-0.423	0.765
hypoxia_3wks	0.534	1.188
hypoxia_6wks	-0.021	1.566
glycerol	0.736	0.278
cholesterol	0.449	-0.34
AJ	0.824	-0.445
Bibs02	0.174	-0.16
Bibs02c	0.246	-0.42
BL6	-0.148	0.101
BL6a	0.756	0.344
BXD01	0.734	0.493
BXD010	0.959	0.367
BXD011	0.899	0.358
BXD03	0.561	0.073
BXD04	1.184	1.237
BXD05	0.862	1.169
BXD06	0.836	0.24
BXD07	0.79	0.855
BXD08	0.618	0.73
BXD09	0.696	0.447
CAST	0.756	-0.384
CCcont	-0.056	0.608
DS01	0.921	-0.226
DS02	1.078	0.287
DS04	0.207	-0.829
DS0c	0.919	0.679
GP01	-0.265	-0.313
GP02	-0.021	-0.321
GP0c	0.665	0.359
NOD	1.642	0.905
NZO	0.581	0.027
PWK	0.715	0.081
H37Rv_KO_CtpC	0.916	0.723
H37Rv_KO_CtpD	1.194	1.029
H37Rv_KO_Rv1272	-0.269	-0.168
H37Rv_KO_SugABC	1.345	0.33
H37Rv_KO_MbtN	0.918	0.11
Trans05	0.278	0.131
macrophage_unactivated	1.042	0.464
IL1	0.0	0.768
Rapamycin	0.341	1.467
Tcell	0.437	0.652
GMCSF	0.591	0.409
IFNab	0.0	0.348
IFNg	1.04	0.35
IFNg_GMCSF1	0.566	0.606
Rv1432_day32	-0.624	0.789
Rv1565c_day32	-0.347	-1.671
secA2_input	0.23	0.611
delta_Rv3594	0.72	0.211
delta_Rv3717	-0.162	0.0
delta_Rv3811	0.744	-0.126
delta_Rv0954	0.549	0.981
PonA1	0.753	0.233
EccD1_KO	0.52	-0.927
EspI_KO	0.893	0.063
PE35_KO	0.983	-0.747
PPE68_KO	0.841	-0.682
glycerol2	-0.13	-0.46
lignocerate	-0.614	-0.342
oleate	0.39	-0.323
phosphatidylcholine	0.088	-0.287
acetate	-0.748	-0.642
glucAc	-1.202	-0.365
Rv0950ko	0.329	0.582
Rv1096ko	0.633	0.431
Rv3684ko	0.121	0.422
delta_otsA_trehalose	-1.184	-1.37