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 Rv2300c/-:

update plot	correlation	link to info on gene
Rv3738c/PPE66	(cc=0.5432)	info on Rv3738c/PPE66
Rv2497c/bkdA	(cc=0.4583)	info on Rv2497c/bkdA
Rv3485c/-	(cc=0.4561)	info on Rv3485c/-
Rv0830/-	(cc=0.4523)	info on Rv0830/-
Rv1141c/echA11	(cc=0.4476)	info on Rv1141c/echA11
Rv0872c/PE_PGRS15	(cc=0.439)	info on Rv0872c/PE_PGRS15
Rv3435c/-	(cc=0.4362)	info on Rv3435c/-
Rv2345/-	(cc=0.4342)	info on Rv2345/-
Rv1153c/omt	(cc=0.43)	info on Rv1153c/omt
Rv3092c/-	(cc=0.4259)	info on Rv3092c/-

Correlation of Rv2300c/- with Rv3435c/-

Normalized LFCs for Rv2300c/-:
(description and provenance of datasets)

	Rv2300c/-	Rv3435c/-
Fe_supp_jason_reseq	-0.223	0.38
low_pH_jason_reseq	-0.714	-1.606
NO_jason_reseq	0.071	0.121
B6_jason_reseq	0.016	0.311
MHCII_jason_reseq	0.209	0.701
Isoniazid02	-0.113	-1.359
Rifampicin4	-0.097	-1.107
Ethambutol3	-0.022	-0.049
Meropenem3	-0.4	-1.004
Vancomycin16	-0.194	-0.939
Rv2680_day32	-1.068	-0.409
H37Rv_KO_MarP	-0.078	0.488
hypoxia_3wks	0.171	-0.542
hypoxia_6wks	0.177	-1.071
glycerol	-0.658	-0.881
cholesterol	-0.495	0.151
AJ	-0.126	0.121
Bibs02	-0.099	-0.164
Bibs02c	0.391	0.385
BL6	0.237	-0.322
BL6a	0.194	-0.235
BXD01	0.109	-0.501
BXD010	0.549	-0.232
BXD011	0.467	-0.345
BXD03	0.122	-0.232
BXD04	0.014	-0.519
BXD05	-0.453	-0.323
BXD06	0.035	-0.683
BXD07	0.259	-0.318
BXD08	0.491	-0.516
BXD09	0.253	-0.487
CAST	0.272	0.235
CCcont	0.236	-0.363
DS01	0.062	0.275
DS02	-0.076	-0.339
DS04	0.169	0.174
DS0c	0.314	-0.03
GP01	0.099	0.041
GP02	0.592	0.585
GP0c	-0.056	-0.572
NOD	0.234	1.434
NZO	0.513	0.721
PWK	0.428	0.361
H37Rv_KO_CtpC	0.364	0.034
H37Rv_KO_CtpD	0.696	0.429
H37Rv_KO_Rv1272	1.149	-0.065
H37Rv_KO_SugABC	0.374	0.359
H37Rv_KO_MbtN	0.381	-0.914
Trans05	0.325	0.396
macrophage_unactivated	0.139	-0.726
IL1	0.332	-0.24
Rapamycin	0.04	-0.433
Tcell	0.029	-0.802
GMCSF	0.174	0.013
IFNab	0.121	-0.713
IFNg	0.484	-0.417
IFNg_GMCSF1	0.531	0.324
Rv1432_day32	0.519	-0.349
Rv1565c_day32	0.21	0.107
secA2_input	0.913	0.081
delta_Rv3594	0.095	-0.349
delta_Rv3717	-0.249	-0.2
delta_Rv3811	-0.397	-0.41
delta_Rv0954	-0.649	0.576
PonA1	-0.321	-0.435
EccD1_KO	0.227	-0.454
EspI_KO	0.465	-0.468
PE35_KO	0.376	-0.554
PPE68_KO	0.118	-0.595
glycerol2	0.738	0.741
lignocerate	0.82	0.494
oleate	1.007	0.686
phosphatidylcholine	0.91	1.046
acetate	0.096	0.539
glucAc	0.207	0.105
Rv0950ko	0.874	-0.036
Rv1096ko	0.214	-0.214
Rv3684ko	0.049	-0.553
delta_otsA_trehalose	0.871	1.447