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 Rv1648/-:

update plot	correlation	link to info on gene
Rv3344c/PE_PGRS49	(cc=0.4907)	info on Rv3344c/PE_PGRS49
Rv2841c/nusA	(cc=0.4844)	info on Rv2841c/nusA
Rv3509c/ilvX	(cc=0.4684)	info on Rv3509c/ilvX
Rv0578c/PE_PGRS7	(cc=0.453)	info on Rv0578c/PE_PGRS7
Rv0741/-	(cc=0.4337)	info on Rv0741/-
Rv0341/iniB	(cc=0.4309)	info on Rv0341/iniB
Rv3825c/pks2	(cc=0.4221)	info on Rv3825c/pks2
Rv1902c/nanT	(cc=0.4172)	info on Rv1902c/nanT
Rv0656c/vapC6	(cc=0.415)	info on Rv0656c/vapC6
Rv0984/moaB2	(cc=0.414)	info on Rv0984/moaB2

Correlation of Rv1648/- with Rv3509c/ilvX

Normalized LFCs for Rv1648/-:
(description and provenance of datasets)

	Rv1648/-	Rv3509c/ilvX
Fe_supp_jason_reseq	-0.204	-0.081
low_pH_jason_reseq	-0.44	-0.375
NO_jason_reseq	0.979	-0.257
B6_jason_reseq	0.273	0.367
MHCII_jason_reseq	0.323	0.362
Isoniazid02	1.326	1.147
Rifampicin4	-0.466	0.55
Ethambutol3	1.125	0.899
Meropenem3	-0.228	0.328
Vancomycin16	0.069	0.727
Rv2680_day32	0.303	-0.207
H37Rv_KO_MarP	-0.347	0.302
hypoxia_3wks	-0.335	-0.104
hypoxia_6wks	0.37	-0.355
glycerol	-0.161	0.699
cholesterol	0.162	0.869
AJ	0.277	0.282
Bibs02	-0.257	0.34
Bibs02c	-0.218	0.45
BL6	0.351	0.502
BL6a	-0.036	0.458
BXD01	-0.386	0.516
BXD010	-0.041	0.03
BXD011	-0.506	0.68
BXD03	-0.019	0.047
BXD04	0.38	0.408
BXD05	-0.382	-0.064
BXD06	-0.208	0.39
BXD07	0.037	0.174
BXD08	-0.628	-0.011
BXD09	-0.459	0.126
CAST	0.394	0.207
CCcont	-0.163	-0.281
DS01	-0.087	0.409
DS02	-0.711	0.28
DS04	0.263	0.835
DS0c	-1.134	0.594
GP01	-0.133	-0.119
GP02	0.943	-0.02
GP0c	0.207	-0.314
NOD	-0.114	0.714
NZO	-0.009	-0.048
PWK	0.358	0.415
H37Rv_KO_CtpC	-0.015	-0.006
H37Rv_KO_CtpD	0.381	0.044
H37Rv_KO_Rv1272	1.044	0.167
H37Rv_KO_SugABC	-0.299	0.471
H37Rv_KO_MbtN	-0.082	0.257
Trans05	0.213	0.094
macrophage_unactivated	-0.694	-0.732
IL1	-0.409	-0.602
Rapamycin	-0.819	-0.868
Tcell	-1.137	-0.459
GMCSF	-0.177	-0.428
IFNab	-1.055	-0.856
IFNg	-0.631	-0.877
IFNg_GMCSF1	-0.691	0.226
Rv1432_day32	0.291	0.756
Rv1565c_day32	-0.262	0.175
secA2_input	0.435	-0.189
delta_Rv3594	0.642	0.783
delta_Rv3717	0.293	0.039
delta_Rv3811	0.419	0.651
delta_Rv0954	1.128	0.915
PonA1	1.114	0.743
EccD1_KO	-0.408	0.072
EspI_KO	-0.017	-0.125
PE35_KO	-0.225	-0.064
PPE68_KO	-0.646	-0.384
glycerol2	-0.56	-0.174
lignocerate	-0.114	-0.358
oleate	-0.909	-0.33
phosphatidylcholine	-0.169	-0.209
acetate	-0.309	-0.849
glucAc	0.085	-0.171
Rv0950ko	0.087	0.612
Rv1096ko	0.443	0.953
Rv3684ko	0.481	0.4
delta_otsA_trehalose	0.314	-0.209