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 Rv1407/fmu:

update plot	correlation	link to info on gene
Rv2301/cut2	(cc=0.5437)	info on Rv2301/cut2
Rv2490c/PE_PGRS43	(cc=0.5291)	info on Rv2490c/PE_PGRS43
Rv2065/cobH	(cc=0.5174)	info on Rv2065/cobH
Rv0038/-	(cc=0.4918)	info on Rv0038/-
Rv0806c/cpsY	(cc=0.4739)	info on Rv0806c/cpsY
Rv3344c/PE_PGRS49	(cc=0.4645)	info on Rv3344c/PE_PGRS49
Rv3649/-	(cc=0.4553)	info on Rv3649/-
Rv0492c/-	(cc=0.4437)	info on Rv0492c/-
Rv0630c/recB	(cc=0.439)	info on Rv0630c/recB
Rv2966c/-	(cc=0.4354)	info on Rv2966c/-

Correlation of Rv1407/fmu with Rv0492c/-

Normalized LFCs for Rv1407/fmu:
(description and provenance of datasets)

	Rv1407/fmu	Rv0492c/-
Fe_supp_jason_reseq	-0.467	0.414
low_pH_jason_reseq	-2.391	-1.029
NO_jason_reseq	0.053	-0.465
B6_jason_reseq	-1.467	-0.441
MHCII_jason_reseq	-0.217	0.039
Isoniazid02	1.15	1.356
Rifampicin4	0.866	1.088
Ethambutol3	-0.123	0.465
Meropenem3	0.089	0.997
Vancomycin16	0.249	0.846
Rv2680_day32	-0.573	0.691
H37Rv_KO_MarP	-0.072	0.349
hypoxia_3wks	-0.159	-0.096
hypoxia_6wks	-0.683	-0.777
glycerol	2.042	0.929
cholesterol	1.49	0.496
AJ	-0.514	0.299
Bibs02	-0.24	0.156
Bibs02c	0.929	0.014
BL6	-0.208	0.707
BL6a	0.23	0.362
BXD01	-0.419	0.304
BXD010	-0.677	0.118
BXD011	-0.962	0.0
BXD03	-0.615	-0.189
BXD04	-0.787	0.0
BXD05	-0.934	-0.562
BXD06	-0.607	-0.187
BXD07	-1.233	0.39
BXD08	-0.246	0.106
BXD09	-0.975	-0.01
CAST	-0.646	0.284
CCcont	0.214	0.373
DS01	0.036	0.833
DS02	-0.173	0.52
DS04	0.698	0.117
DS0c	-1.571	-0.016
GP01	0.902	1.039
GP02	-0.34	0.781
GP0c	-0.474	0.521
NOD	-1.022	0.33
NZO	-0.331	0.053
PWK	-0.435	0.335
H37Rv_KO_CtpC	-0.859	0.588
H37Rv_KO_CtpD	-0.407	0.855
H37Rv_KO_Rv1272	0.346	0.233
H37Rv_KO_SugABC	0.42	1.094
H37Rv_KO_MbtN	0.148	0.947
Trans05	0.717	0.641
macrophage_unactivated	-0.451	-0.066
IL1	-0.7	0.181
Rapamycin	0.476	-0.043
Tcell	-0.274	-0.023
GMCSF	0.071	0.61
IFNab	-0.166	0.206
IFNg	-1.184	0.075
IFNg_GMCSF1	-0.742	0.129
Rv1432_day32	0.13	0.913
Rv1565c_day32	-0.063	0.046
secA2_input	-0.142	0.327
delta_Rv3594	0.951	0.083
delta_Rv3717	1.682	-0.253
delta_Rv3811	0.546	0.091
delta_Rv0954	0.788	0.43
PonA1	-0.631	0.384
EccD1_KO	0.23	0.263
EspI_KO	-0.667	-0.279
PE35_KO	0.904	-0.286
PPE68_KO	-0.141	-0.019
glycerol2	-0.832	0.102
lignocerate	-0.57	-0.214
oleate	-0.291	0.58
phosphatidylcholine	-0.287	0.092
acetate	0.057	-0.625
glucAc	-0.112	-0.348
Rv0950ko	1.089	0.549
Rv1096ko	1.526	0.621
Rv3684ko	0.603	0.576
delta_otsA_trehalose	-1.541	-0.229