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 Rv3900c/-:

update plot	correlation	link to info on gene
Rv3537/kstD	(cc=0.5508)	info on Rv3537/kstD
Rv1729c/-	(cc=0.4953)	info on Rv1729c/-
Rv3762c/-	(cc=0.4834)	info on Rv3762c/-
Rv0250c/-	(cc=0.4772)	info on Rv0250c/-
Rv1059/-	(cc=0.4726)	info on Rv1059/-
Rv2929/-	(cc=0.4714)	info on Rv2929/-
Rv3429/PPE59	(cc=0.4696)	info on Rv3429/PPE59
Rv3146/nuoB	(cc=0.4689)	info on Rv3146/nuoB
Rv1870c/-	(cc=0.461)	info on Rv1870c/-
Rv1207/folP2	(cc=0.4518)	info on Rv1207/folP2

Correlation of Rv3900c/- with Rv0250c/-

Normalized LFCs for Rv3900c/-:
(description and provenance of datasets)

	Rv3900c/-	Rv0250c/-
Fe_supp_jason_reseq	-0.406	0.988
low_pH_jason_reseq	0.632	1.061
NO_jason_reseq	-0.352	-0.147
B6_jason_reseq	-0.285	-0.768
MHCII_jason_reseq	-0.876	-0.532
Isoniazid02	-0.226	0.343
Rifampicin4	0.544	0.85
Ethambutol3	0.946	0.472
Meropenem3	1.216	0.879
Vancomycin16	0.228	1.443
Rv2680_day32	-0.763	0.412
H37Rv_KO_MarP	0.679	0.265
hypoxia_3wks	0.49	0.71
hypoxia_6wks	-0.077	-0.073
glycerol	-0.24	0.051
cholesterol	-0.243	0.174
AJ	-0.439	1.496
Bibs02	-0.631	-0.302
Bibs02c	-0.878	-3.086
BL6	0.272	1.812
BL6a	-0.105	0.283
BXD01	0.446	1.602
BXD010	0.597	0.911
BXD011	0.116	0.316
BXD03	0.236	1.795
BXD04	0.63	2.336
BXD05	0.225	1.498
BXD06	0.749	2.132
BXD07	0.413	1.59
BXD08	0.497	1.168
BXD09	0.7	2.282
CAST	0.117	-0.38
CCcont	0.838	2.393
DS01	-0.021	-1.222
DS02	-0.884	-0.425
DS04	0.748	4.015
DS0c	-0.671	-2.982
GP01	0.801	2.633
GP02	-0.257	1.875
GP0c	0.689	2.112
NOD	0.094	-0.981
NZO	-0.712	-0.39
PWK	-0.196	0.912
H37Rv_KO_CtpC	-0.042	2.749
H37Rv_KO_CtpD	1.454	3.664
H37Rv_KO_Rv1272	0.336	0.46
H37Rv_KO_SugABC	0.8	1.496
H37Rv_KO_MbtN	0.202	3.379
Trans05	-0.034	2.101
macrophage_unactivated	0.451	-0.06
IL1	0.311	0.205
Rapamycin	0.368	0.577
Tcell	-0.137	-0.681
GMCSF	0.214	1.053
IFNab	0.339	-1.536
IFNg	0.0	1.486
IFNg_GMCSF1	-0.647	1.103
Rv1432_day32	-0.469	0.0
Rv1565c_day32	-0.058	0.0
secA2_input	0.177	-0.581
delta_Rv3594	-0.054	0.696
delta_Rv3717	-0.736	1.34
delta_Rv3811	0.241	2.043
delta_Rv0954	-0.261	2.191
PonA1	-0.07	-0.031
EccD1_KO	-0.582	0.059
EspI_KO	-0.884	0.376
PE35_KO	-0.137	-0.251
PPE68_KO	-0.086	0.342
glycerol2	0.294	-0.806
lignocerate	0.203	-1.548
oleate	0.089	-0.121
phosphatidylcholine	-0.057	-0.088
acetate	-0.361	0.229
glucAc	-0.205	-1.367
Rv0950ko	0.109	1.978
Rv1096ko	-0.802	1.595
Rv3684ko	-0.098	1.67
delta_otsA_trehalose	-0.73	-0.897