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 Rv0134/ephF:

update plot	correlation	link to info on gene
Rv2914c/pknI	(cc=0.549)	info on Rv2914c/pknI
Rv3896c/-	(cc=0.5341)	info on Rv3896c/-
Rv0327c/cyp135A1	(cc=0.5183)	info on Rv0327c/cyp135A1
Rv3026c/-	(cc=0.504)	info on Rv3026c/-
Rv0530/-	(cc=0.4818)	info on Rv0530/-
Rv3786c/-	(cc=0.4778)	info on Rv3786c/-
Rv3522/ltp4	(cc=0.473)	info on Rv3522/ltp4
Rv0897c/-	(cc=0.4604)	info on Rv0897c/-
Rv0858c/dapC	(cc=0.4531)	info on Rv0858c/dapC
Rv0648/-	(cc=0.4515)	info on Rv0648/-

Correlation of Rv0134/ephF with Rv0530/-

Normalized LFCs for Rv0134/ephF:
(description and provenance of datasets)

	Rv0134/ephF	Rv0530/-
Fe_supp_jason_reseq	-0.568	-0.276
low_pH_jason_reseq	-0.688	-0.321
NO_jason_reseq	0.391	0.236
B6_jason_reseq	0.413	0.625
MHCII_jason_reseq	0.941	0.96
Isoniazid02	-0.345	0.292
Rifampicin4	0.0	-0.222
Ethambutol3	-0.461	0.582
Meropenem3	0.271	0.265
Vancomycin16	-0.273	-0.838
Rv2680_day32	-0.09	-0.954
H37Rv_KO_MarP	0.213	0.12
hypoxia_3wks	-0.478	-0.57
hypoxia_6wks	-0.106	-0.23
glycerol	0.168	-0.044
cholesterol	-0.859	-0.614
AJ	0.077	0.309
Bibs02	-0.449	0.351
Bibs02c	0.759	0.333
BL6	0.587	-0.4
BL6a	0.639	0.042
BXD01	-0.265	-0.154
BXD010	-0.255	-0.646
BXD011	0.421	-0.259
BXD03	0.226	-0.672
BXD04	-0.24	0.031
BXD05	0.463	-0.544
BXD06	0.175	-0.618
BXD07	-0.048	-0.137
BXD08	0.152	-0.277
BXD09	0.292	-0.568
CAST	0.792	0.864
CCcont	-0.331	-0.12
DS01	0.229	1.025
DS02	0.249	-0.154
DS04	1.152	0.309
DS0c	0.445	0.787
GP01	0.371	0.37
GP02	1.127	1.026
GP0c	0.279	0.212
NOD	0.404	0.029
NZO	0.345	0.026
PWK	0.566	0.742
H37Rv_KO_CtpC	-0.114	-0.435
H37Rv_KO_CtpD	-0.348	0.327
H37Rv_KO_Rv1272	-0.224	-1.102
H37Rv_KO_SugABC	0.588	0.252
H37Rv_KO_MbtN	0.961	0.125
Trans05	-0.302	-0.813
macrophage_unactivated	0.069	-0.331
IL1	0.018	0.208
Rapamycin	-0.034	0.675
Tcell	0.072	-0.469
GMCSF	1.098	0.364
IFNab	-0.121	-0.46
IFNg	0.596	-0.059
IFNg_GMCSF1	1.037	1.345
Rv1432_day32	0.224	0.849
Rv1565c_day32	0.188	-0.518
secA2_input	0.297	0.333
delta_Rv3594	-0.197	-0.393
delta_Rv3717	0.127	0.345
delta_Rv3811	-0.132	-0.256
delta_Rv0954	-0.098	0.224
PonA1	0.698	0.391
EccD1_KO	0.421	-0.444
EspI_KO	-0.351	-0.536
PE35_KO	-0.621	-0.099
PPE68_KO	-0.682	-0.55
glycerol2	0.265	0.015
lignocerate	0.952	0.961
oleate	-0.6	-0.472
phosphatidylcholine	0.326	0.353
acetate	0.51	0.251
glucAc	0.706	0.367
Rv0950ko	0.986	0.244
Rv1096ko	1.692	0.29
Rv3684ko	1.657	0.39
delta_otsA_trehalose	-0.613	0.888