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 Rv0604/lpqO:

update plot	correlation	link to info on gene
Rv2879c/-	(cc=0.519)	info on Rv2879c/-
Rv1249c/-	(cc=0.4964)	info on Rv1249c/-
Rv1442/bisC	(cc=0.4954)	info on Rv1442/bisC
Rv3532/PPE61	(cc=0.4866)	info on Rv3532/PPE61
Rv0302/-	(cc=0.4756)	info on Rv0302/-
Rv2007c/fdxA	(cc=0.4718)	info on Rv2007c/fdxA
Rv2880c/-	(cc=0.4691)	info on Rv2880c/-
Rv0015c/pknA	(cc=0.4678)	info on Rv0015c/pknA
Rv0269c/-	(cc=0.4656)	info on Rv0269c/-
Rv0061c/-	(cc=0.4604)	info on Rv0061c/-

Correlation of Rv0604/lpqO with Rv2880c/-

Normalized LFCs for Rv0604/lpqO:
(description and provenance of datasets)

	Rv0604/lpqO	Rv2880c/-
Fe_supp_jason_reseq	1.159	-0.338
low_pH_jason_reseq	-1.474	-0.813
NO_jason_reseq	-2.195	0.512
B6_jason_reseq	0.798	0.677
MHCII_jason_reseq	1.287	0.254
Isoniazid02	0.038	0.058
Rifampicin4	0.347	0.791
Ethambutol3	-0.17	0.495
Meropenem3	0.048	-0.01
Vancomycin16	0.0	0.615
Rv2680_day32	-0.525	-0.55
H37Rv_KO_MarP	0.116	0.065
hypoxia_3wks	0.53	-0.299
hypoxia_6wks	-0.507	-1.002
glycerol	1.27	-0.101
cholesterol	0.077	-0.136
AJ	0.729	0.168
Bibs02	1.249	0.87
Bibs02c	0.896	0.915
BL6	0.144	0.319
BL6a	0.027	0.178
BXD01	0.39	-0.144
BXD010	-0.118	0.043
BXD011	-0.94	-0.47
BXD03	-0.115	0.121
BXD04	-1.037	-0.023
BXD05	0.089	0.514
BXD06	-0.78	-0.332
BXD07	-0.46	0.328
BXD08	0.509	0.133
BXD09	-0.416	0.187
CAST	-0.112	0.11
CCcont	0.098	-0.302
DS01	0.731	0.392
DS02	0.684	0.469
DS04	0.839	0.937
DS0c	0.404	0.104
GP01	0.0	0.351
GP02	-0.262	-0.802
GP0c	-0.101	-0.251
NOD	-0.921	-0.138
NZO	0.118	0.279
PWK	-0.124	0.418
H37Rv_KO_CtpC	-1.291	-0.062
H37Rv_KO_CtpD	-0.532	0.341
H37Rv_KO_Rv1272	-1.06	-0.253
H37Rv_KO_SugABC	-1.802	0.362
H37Rv_KO_MbtN	-0.819	-0.839
Trans05	0.462	0.25
macrophage_unactivated	1.18	-0.17
IL1	0.027	0.578
Rapamycin	-0.792	0.16
Tcell	-0.274	-0.381
GMCSF	0.14	0.285
IFNab	-0.342	0.048
IFNg	-1.085	0.289
IFNg_GMCSF1	2.124	0.867
Rv1432_day32	1.395	0.997
Rv1565c_day32	1.058	0.27
secA2_input	-0.221	0.088
delta_Rv3594	-0.857	-1.169
delta_Rv3717	-1.05	-1.277
delta_Rv3811	-1.689	-1.097
delta_Rv0954	-0.724	-1.151
PonA1	-2.328	-0.733
EccD1_KO	0.506	0.115
EspI_KO	-0.24	0.753
PE35_KO	0.175	0.907
PPE68_KO	0.637	0.653
glycerol2	0.726	0.179
lignocerate	1.142	-0.018
oleate	1.353	0.252
phosphatidylcholine	1.452	0.081
acetate	0.843	-0.434
glucAc	0.631	-0.54
Rv0950ko	0.799	0.757
Rv1096ko	0.124	0.072
Rv3684ko	0.665	0.0
delta_otsA_trehalose	1.318	0.753