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 Rv3452/cut4:

update plot	correlation	link to info on gene
Rv3470c/ilvB2	(cc=0.4339)	info on Rv3470c/ilvB2
Rv0476/-	(cc=0.4072)	info on Rv0476/-
Rv0492c/-	(cc=0.3998)	info on Rv0492c/-
Rv2790c/ltp1	(cc=0.3959)	info on Rv2790c/ltp1
Rv2590/fadD9	(cc=0.3957)	info on Rv2590/fadD9
Rv1523/-	(cc=0.3898)	info on Rv1523/-
Rv0762c/-	(cc=0.3832)	info on Rv0762c/-
Rv2836c/dinF	(cc=0.3812)	info on Rv2836c/dinF
Rv3835/-	(cc=0.381)	info on Rv3835/-
Rv1489/-	(cc=0.3804)	info on Rv1489/-

Correlation of Rv3452/cut4 with Rv3470c/ilvB2

Normalized LFCs for Rv3452/cut4:
(description and provenance of datasets)

	Rv3452/cut4	Rv3470c/ilvB2
Fe_supp_jason_reseq	0.373	-0.415
low_pH_jason_reseq	-1.705	-0.31
NO_jason_reseq	-0.173	-0.034
B6_jason_reseq	-1.074	-1.714
MHCII_jason_reseq	-0.37	-0.591
Isoniazid02	0.857	0.333
Rifampicin4	1.17	0.23
Ethambutol3	0.421	0.103
Meropenem3	1.543	0.444
Vancomycin16	0.825	0.297
Rv2680_day32	0.819	-0.351
H37Rv_KO_MarP	0.224	0.35
hypoxia_3wks	0.044	0.327
hypoxia_6wks	0.382	-0.752
glycerol	0.831	0.391
cholesterol	-0.722	0.357
AJ	0.398	0.8
Bibs02	0.257	-0.589
Bibs02c	-0.183	-0.07
BL6	0.99	1.148
BL6a	0.476	0.462
BXD01	0.821	0.737
BXD010	0.553	0.23
BXD011	0.131	0.709
BXD03	0.407	0.686
BXD04	0.309	1.232
BXD05	1.164	0.399
BXD06	0.055	0.537
BXD07	0.359	0.15
BXD08	0.476	1.282
BXD09	0.485	0.467
CAST	0.452	-0.038
CCcont	0.77	0.817
DS01	0.914	0.038
DS02	0.427	-0.224
DS04	0.618	0.239
DS0c	-0.398	-0.798
GP01	1.36	1.466
GP02	-0.698	-0.659
GP0c	-0.184	-0.573
NOD	-0.613	0.434
NZO	0.321	0.275
PWK	-0.024	0.557
H37Rv_KO_CtpC	0.913	0.994
H37Rv_KO_CtpD	-0.503	0.391
H37Rv_KO_Rv1272	-0.846	0.329
H37Rv_KO_SugABC	1.139	0.854
H37Rv_KO_MbtN	1.986	0.573
Trans05	0.815	0.967
macrophage_unactivated	1.228	0.707
IL1	-0.454	-0.893
Rapamycin	-0.068	-0.365
Tcell	0.0	-0.489
GMCSF	0.042	-0.232
IFNab	0.55	-0.088
IFNg	0.409	-0.155
IFNg_GMCSF1	1.197	0.386
Rv1432_day32	-0.351	0.378
Rv1565c_day32	0.215	0.27
secA2_input	-0.543	-0.703
delta_Rv3594	0.012	-0.956
delta_Rv3717	-0.059	-0.06
delta_Rv3811	0.717	0.427
delta_Rv0954	-0.165	0.176
PonA1	1.252	-0.235
EccD1_KO	0.454	-0.595
EspI_KO	0.291	-0.337
PE35_KO	-0.073	0.082
PPE68_KO	-0.214	-0.186
glycerol2	0.817	0.017
lignocerate	0.877	-0.088
oleate	1.375	-0.034
phosphatidylcholine	1.111	0.143
acetate	0.218	-0.203
glucAc	0.259	-0.324
Rv0950ko	-0.181	-0.19
Rv1096ko	0.142	0.808
Rv3684ko	0.255	0.527
delta_otsA_trehalose	-1.347	0.212