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 Rv3649/-:

update plot	correlation	link to info on gene
Rv3509c/ilvX	(cc=0.4849)	info on Rv3509c/ilvX
Rv2089c/pepE	(cc=0.4627)	info on Rv2089c/pepE
Rv2490c/PE_PGRS43	(cc=0.4627)	info on Rv2490c/PE_PGRS43
Rv1407/fmu	(cc=0.4553)	info on Rv1407/fmu
Rv2974c/-	(cc=0.4521)	info on Rv2974c/-
Rv1075c/-	(cc=0.4499)	info on Rv1075c/-
Rv1135c/PPE16	(cc=0.4448)	info on Rv1135c/PPE16
Rv0203/-	(cc=0.442)	info on Rv0203/-
Rv2340c/PE_PGRS39	(cc=0.4406)	info on Rv2340c/PE_PGRS39
Rv2585c/-	(cc=0.4399)	info on Rv2585c/-

Correlation of Rv3649/- with Rv3509c/ilvX

Normalized LFCs for Rv3649/-:
(description and provenance of datasets)

	Rv3649/-	Rv3509c/ilvX
Fe_supp_jason_reseq	0.332	-0.081
low_pH_jason_reseq	-0.527	-0.375
NO_jason_reseq	0.286	-0.257
B6_jason_reseq	1.045	0.367
MHCII_jason_reseq	1.194	0.362
Isoniazid02	0.469	1.147
Rifampicin4	1.243	0.55
Ethambutol3	1.043	0.899
Meropenem3	0.936	0.328
Vancomycin16	0.95	0.727
Rv2680_day32	-0.617	-0.207
H37Rv_KO_MarP	-0.731	0.302
hypoxia_3wks	0.223	-0.104
hypoxia_6wks	0.077	-0.355
glycerol	0.426	0.699
cholesterol	0.791	0.869
AJ	0.035	0.282
Bibs02	1.252	0.34
Bibs02c	0.621	0.45
BL6	0.773	0.502
BL6a	-0.032	0.458
BXD01	0.387	0.516
BXD010	0.588	0.03
BXD011	-0.082	0.68
BXD03	-0.204	0.047
BXD04	-0.039	0.408
BXD05	0.041	-0.064
BXD06	0.041	0.39
BXD07	0.042	0.174
BXD08	-0.13	-0.011
BXD09	-0.29	0.126
CAST	-0.265	0.207
CCcont	0.257	-0.281
DS01	0.672	0.409
DS02	0.999	0.28
DS04	1.148	0.835
DS0c	0.767	0.594
GP01	-0.204	-0.119
GP02	-0.386	-0.02
GP0c	0.503	-0.314
NOD	-0.107	0.714
NZO	-0.095	-0.048
PWK	0.119	0.415
H37Rv_KO_CtpC	-1.203	-0.006
H37Rv_KO_CtpD	0.0	0.044
H37Rv_KO_Rv1272	0.146	0.167
H37Rv_KO_SugABC	0.117	0.471
H37Rv_KO_MbtN	0.42	0.257
Trans05	0.52	0.094
macrophage_unactivated	-0.537	-0.732
IL1	0.0	-0.602
Rapamycin	0.0	-0.868
Tcell	0.13	-0.459
GMCSF	0.401	-0.428
IFNab	-0.06	-0.856
IFNg	-0.337	-0.877
IFNg_GMCSF1	0.305	0.226
Rv1432_day32	0.329	0.756
Rv1565c_day32	-0.463	0.175
secA2_input	-0.049	-0.189
delta_Rv3594	0.263	0.783
delta_Rv3717	1.061	0.039
delta_Rv3811	0.97	0.651
delta_Rv0954	0.249	0.915
PonA1	0.199	0.743
EccD1_KO	1.043	0.072
EspI_KO	-0.148	-0.125
PE35_KO	0.487	-0.064
PPE68_KO	0.314	-0.384
glycerol2	-0.321	-0.174
lignocerate	-0.363	-0.358
oleate	-0.027	-0.33
phosphatidylcholine	-0.258	-0.209
acetate	-0.271	-0.849
glucAc	0.726	-0.171
Rv0950ko	0.443	0.612
Rv1096ko	1.212	0.953
Rv3684ko	0.704	0.4
delta_otsA_trehalose	-0.564	-0.209