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 Rv2869c/rip:

update plot	correlation	link to info on gene
Rv1860/apa	(cc=0.6913)	info on Rv1860/apa
Rv2363/amiA2	(cc=0.6798)	info on Rv2363/amiA2
Rv1006/-	(cc=0.6767)	info on Rv1006/-
Rv2051c/ppm1	(cc=0.6433)	info on Rv2051c/ppm1
Rv1685c/-	(cc=0.6277)	info on Rv1685c/-
Rv3207c/-	(cc=0.6271)	info on Rv3207c/-
Rv2553c/-	(cc=0.599)	info on Rv2553c/-
Rv1512/epiA	(cc=0.5966)	info on Rv1512/epiA
Rv3102c/ftsE	(cc=0.5853)	info on Rv3102c/ftsE
Rv0437c/psd	(cc=0.5822)	info on Rv0437c/psd

Correlation of Rv2869c/rip with Rv1860/apa

Normalized LFCs for Rv2869c/rip:
(description and provenance of datasets)

	Rv2869c/rip	Rv1860/apa
Fe_supp_jason_reseq	2.823	3.272
low_pH_jason_reseq	-0.231	-0.457
NO_jason_reseq	-0.362	0.129
B6_jason_reseq	-0.153	0.054
MHCII_jason_reseq	-0.135	-0.101
Isoniazid02	-0.361	-1.043
Rifampicin4	-2.507	-5.772
Ethambutol3	0.482	0.061
Meropenem3	-0.528	-0.701
Vancomycin16	-2.09	-5.858
Rv2680_day32	-1.078	1.123
H37Rv_KO_MarP	-4.082	-3.981
hypoxia_3wks	-2.504	-1.958
hypoxia_6wks	-1.599	-3.197
glycerol	0.0	1.934
cholesterol	0.614	1.239
AJ	0.0	-0.541
Bibs02	0.0	0.898
Bibs02c	0.0	0.838
BL6	0.0	-0.822
BL6a	0.0	-0.55
BXD01	0.0	-1.087
BXD010	0.0	-1.021
BXD011	0.127	-0.643
BXD03	0.0	-0.934
BXD04	0.0	-1.131
BXD05	0.0	-0.123
BXD06	0.0	-1.014
BXD07	0.0	-1.156
BXD08	0.0	-0.564
BXD09	0.0	-0.75
CAST	0.0	-1.59
CCcont	2.313	1.056
DS01	0.0	0.801
DS02	0.0	0.737
DS04	0.37	1.248
DS0c	0.0	-0.652
GP01	0.0	-0.682
GP02	0.0	-1.0
GP0c	0.0	-1.085
NOD	0.0	-1.01
NZO	0.0	0.626
PWK	0.0	-0.544
H37Rv_KO_CtpC	0.998	1.966
H37Rv_KO_CtpD	0.445	-0.751
H37Rv_KO_Rv1272	0.0	0.141
H37Rv_KO_SugABC	0.42	1.422
H37Rv_KO_MbtN	1.07	0.349
Trans05	0.0	1.414
macrophage_unactivated	0.0	0.609
IL1	-0.374	-0.78
Rapamycin	0.0	-0.328
Tcell	-0.411	-0.857
GMCSF	-0.333	0.09
IFNab	1.255	-0.553
IFNg	0.593	-0.286
IFNg_GMCSF1	-0.396	-0.22
Rv1432_day32	-0.884	1.0
Rv1565c_day32	0.0	0.351
secA2_input	2.826	1.19
delta_Rv3594	0.783	1.386
delta_Rv3717	0.824	0.839
delta_Rv3811	0.376	1.423
delta_Rv0954	1.569	2.022
PonA1	0.069	0.397
EccD1_KO	-0.549	0.918
EspI_KO	-0.827	1.189
PE35_KO	0.435	1.021
PPE68_KO	0.912	1.315
glycerol2	-0.193	-0.563
lignocerate	-0.168	-0.521
oleate	-0.196	-0.173
phosphatidylcholine	-0.193	-1.097
acetate	0.0	0.648
glucAc	-0.143	0.153
Rv0950ko	-1.538	-1.049
Rv1096ko	-0.703	-0.98
Rv3684ko	-0.943	0.138
delta_otsA_trehalose	-0.041	-0.86