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 Rv1527c/pks5:

update plot	correlation	link to info on gene
Rv1838c/vapC13	(cc=0.5927)	info on Rv1838c/vapC13
Rv2123/PPE37	(cc=0.534)	info on Rv2123/PPE37
Rv0278c/PE_PGRS3	(cc=0.5279)	info on Rv0278c/PE_PGRS3
Rv0969/ctpV	(cc=0.5033)	info on Rv0969/ctpV
Rv1834/lipZ	(cc=0.5007)	info on Rv1834/lipZ
Rv1760/-	(cc=0.4985)	info on Rv1760/-
Rv2177c/-	(cc=0.4975)	info on Rv2177c/-
Rv1625c/cya	(cc=0.4968)	info on Rv1625c/cya
Rv1263/amiB2	(cc=0.4927)	info on Rv1263/amiB2
Rv2025c/-	(cc=0.4908)	info on Rv2025c/-

Correlation of Rv1527c/pks5 with Rv0278c/PE_PGRS3

Normalized LFCs for Rv1527c/pks5:
(description and provenance of datasets)

	Rv1527c/pks5	Rv0278c/PE_PGRS3
Fe_supp_jason_reseq	0.175	-0.425
low_pH_jason_reseq	-0.587	-0.853
NO_jason_reseq	-0.155	-0.249
B6_jason_reseq	0.181	-0.18
MHCII_jason_reseq	0.229	0.931
Isoniazid02	-0.015	-0.119
Rifampicin4	-0.057	0.412
Ethambutol3	0.225	0.711
Meropenem3	0.915	1.444
Vancomycin16	-0.056	0.0
Rv2680_day32	-0.199	0.83
H37Rv_KO_MarP	0.189	0.416
hypoxia_3wks	0.159	-0.427
hypoxia_6wks	0.294	-0.223
glycerol	0.196	1.118
cholesterol	0.013	1.118
AJ	0.622	0.341
Bibs02	0.15	1.095
Bibs02c	0.477	0.041
BL6	0.251	-0.701
BL6a	0.066	-1.045
BXD01	-0.215	-0.192
BXD010	0.021	-0.594
BXD011	-0.262	-0.553
BXD03	-0.108	-0.902
BXD04	-0.508	-1.024
BXD05	0.022	-0.544
BXD06	-0.39	-1.105
BXD07	-0.036	-0.269
BXD08	0.022	-0.197
BXD09	-0.304	-0.342
CAST	-0.12	-0.045
CCcont	0.025	-0.122
DS01	0.554	-0.144
DS02	0.126	0.759
DS04	0.455	0.382
DS0c	0.325	-0.178
GP01	1.712	0.852
GP02	0.477	0.732
GP0c	0.555	0.169
NOD	0.304	-0.602
NZO	0.314	-0.039
PWK	-0.017	0.185
H37Rv_KO_CtpC	0.314	-0.705
H37Rv_KO_CtpD	0.143	-0.077
H37Rv_KO_Rv1272	0.415	0.081
H37Rv_KO_SugABC	0.611	0.146
H37Rv_KO_MbtN	-0.13	-0.578
Trans05	0.289	0.723
macrophage_unactivated	-0.158	-0.211
IL1	-0.074	-1.783
Rapamycin	-0.114	-1.013
Tcell	-0.081	-1.075
GMCSF	0.19	-0.982
IFNab	-0.151	-0.998
IFNg	-0.134	-0.882
IFNg_GMCSF1	0.189	-0.211
Rv1432_day32	0.216	0.24
Rv1565c_day32	-0.104	-0.622
secA2_input	0.523	-0.028
delta_Rv3594	0.021	0.02
delta_Rv3717	-0.374	0.156
delta_Rv3811	0.312	-0.498
delta_Rv0954	-0.172	-0.634
PonA1	0.492	0.479
EccD1_KO	0.089	0.095
EspI_KO	0.262	0.442
PE35_KO	0.23	0.213
PPE68_KO	0.378	0.234
glycerol2	0.46	2.123
lignocerate	0.673	2.776
oleate	0.373	0.0
phosphatidylcholine	0.696	2.122
acetate	0.845	3.238
glucAc	0.441	2.725
Rv0950ko	0.422	0.0
Rv1096ko	0.311	0.247
Rv3684ko	0.498	-0.111
delta_otsA_trehalose	0.551	-1.199