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 Rv2836c/dinF

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

	Rv3452/cut4	Rv2836c/dinF
Fe_supp_jason_reseq	0.373	-0.112
low_pH_jason_reseq	-1.705	-0.482
NO_jason_reseq	-0.173	0.045
B6_jason_reseq	-1.074	-0.442
MHCII_jason_reseq	-0.37	-0.052
Isoniazid02	0.857	1.072
Rifampicin4	1.17	0.967
Ethambutol3	0.421	0.762
Meropenem3	1.543	1.198
Vancomycin16	0.825	1.25
Rv2680_day32	0.819	0.075
H37Rv_KO_MarP	0.224	-0.371
hypoxia_3wks	0.044	-0.686
hypoxia_6wks	0.382	-1.117
glycerol	0.831	0.348
cholesterol	-0.722	-0.069
AJ	0.398	-0.308
Bibs02	0.257	0.605
Bibs02c	-0.183	0.305
BL6	0.99	0.094
BL6a	0.476	0.03
BXD01	0.821	0.598
BXD010	0.553	0.35
BXD011	0.131	0.019
BXD03	0.407	-0.156
BXD04	0.309	0.775
BXD05	1.164	0.177
BXD06	0.055	-0.086
BXD07	0.359	-0.022
BXD08	0.476	0.347
BXD09	0.485	0.0
CAST	0.452	0.486
CCcont	0.77	0.609
DS01	0.914	0.809
DS02	0.427	-0.176
DS04	0.618	-0.093
DS0c	-0.398	1.376
GP01	1.36	1.144
GP02	-0.698	0.294
GP0c	-0.184	0.53
NOD	-0.613	-0.421
NZO	0.321	-1.477
PWK	-0.024	-0.192
H37Rv_KO_CtpC	0.913	0.122
H37Rv_KO_CtpD	-0.503	-0.262
H37Rv_KO_Rv1272	-0.846	0.064
H37Rv_KO_SugABC	1.139	0.465
H37Rv_KO_MbtN	1.986	1.034
Trans05	0.815	-0.084
macrophage_unactivated	1.228	0.401
IL1	-0.454	0.67
Rapamycin	-0.068	0.574
Tcell	0.0	0.609
GMCSF	0.042	0.335
IFNab	0.55	0.0
IFNg	0.409	0.847
IFNg_GMCSF1	1.197	0.996
Rv1432_day32	-0.351	-0.177
Rv1565c_day32	0.215	0.913
secA2_input	-0.543	0.291
delta_Rv3594	0.012	0.618
delta_Rv3717	-0.059	0.082
delta_Rv3811	0.717	-0.101
delta_Rv0954	-0.165	-0.119
PonA1	1.252	0.427
EccD1_KO	0.454	0.766
EspI_KO	0.291	0.665
PE35_KO	-0.073	-0.295
PPE68_KO	-0.214	0.243
glycerol2	0.817	0.6
lignocerate	0.877	1.511
oleate	1.375	-0.037
phosphatidylcholine	1.111	1.017
acetate	0.218	2.663
glucAc	0.259	1.35
Rv0950ko	-0.181	0.112
Rv1096ko	0.142	-0.115
Rv3684ko	0.255	-0.062
delta_otsA_trehalose	-1.347	-0.737