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 Rv0892/-

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

	Rv0778/cyp126	Rv0892/-
Fe_supp_jason_reseq	2.014	2.0
low_pH_jason_reseq	-0.571	0.146
NO_jason_reseq	-0.651	0.0
B6_jason_reseq	0.523	1.447
MHCII_jason_reseq	0.706	0.126
Isoniazid02	-0.525	-0.333
Rifampicin4	0.157	0.114
Ethambutol3	-0.403	0.0
Meropenem3	0.298	1.435
Vancomycin16	0.154	0.218
Rv2680_day32	0.508	-0.406
H37Rv_KO_MarP	-0.423	0.0
hypoxia_3wks	0.534	0.207
hypoxia_6wks	-0.021	-0.228
glycerol	0.736	-0.831
cholesterol	0.449	0.035
AJ	0.824	0.0
Bibs02	0.174	0.699
Bibs02c	0.246	1.096
BL6	-0.148	0.796
BL6a	0.756	1.336
BXD01	0.734	0.408
BXD010	0.959	1.116
BXD011	0.899	0.53
BXD03	0.561	0.805
BXD04	1.184	0.554
BXD05	0.862	0.745
BXD06	0.836	0.884
BXD07	0.79	0.881
BXD08	0.618	0.317
BXD09	0.696	0.856
CAST	0.756	0.592
CCcont	-0.056	0.0
DS01	0.921	1.237
DS02	1.078	0.904
DS04	0.207	0.807
DS0c	0.919	0.792
GP01	-0.265	-0.559
GP02	-0.021	-0.507
GP0c	0.665	-0.065
NOD	1.642	0.62
NZO	0.581	-1.215
PWK	0.715	0.226
H37Rv_KO_CtpC	0.916	0.99
H37Rv_KO_CtpD	1.194	1.402
H37Rv_KO_Rv1272	-0.269	0.539
H37Rv_KO_SugABC	1.345	1.063
H37Rv_KO_MbtN	0.918	0.14
Trans05	0.278	0.741
macrophage_unactivated	1.042	0.193
IL1	0.0	0.881
Rapamycin	0.341	0.126
Tcell	0.437	-0.068
GMCSF	0.591	-0.055
IFNab	0.0	-0.063
IFNg	1.04	0.0
IFNg_GMCSF1	0.566	0.314
Rv1432_day32	-0.624	-0.553
Rv1565c_day32	-0.347	-0.227
secA2_input	0.23	-0.639
delta_Rv3594	0.72	-0.05
delta_Rv3717	-0.162	-0.174
delta_Rv3811	0.744	-0.1
delta_Rv0954	0.549	0.238
PonA1	0.753	0.037
EccD1_KO	0.52	0.704
EspI_KO	0.893	0.539
PE35_KO	0.983	0.837
PPE68_KO	0.841	0.442
glycerol2	-0.13	-0.923
lignocerate	-0.614	-0.947
oleate	0.39	-0.034
phosphatidylcholine	0.088	-0.536
acetate	-0.748	-0.485
glucAc	-1.202	-1.084
Rv0950ko	0.329	0.887
Rv1096ko	0.633	0.271
Rv3684ko	0.121	0.075
delta_otsA_trehalose	-1.184	-1.314