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 Rv3892c/PPE69:

update plot	correlation	link to info on gene
Rv2340c/PE_PGRS39	(cc=0.6054)	info on Rv2340c/PE_PGRS39
Rv3728/-	(cc=0.526)	info on Rv3728/-
Rv1066/-	(cc=0.5115)	info on Rv1066/-
Rv1468c/PE_PGRS29	(cc=0.4789)	info on Rv1468c/PE_PGRS29
Rv2141c/-	(cc=0.4777)	info on Rv2141c/-
Rv3879c/espK	(cc=0.4721)	info on Rv3879c/espK
Rv3532/PPE61	(cc=0.4668)	info on Rv3532/PPE61
Rv0218/-	(cc=0.4667)	info on Rv0218/-
Rv0075/-	(cc=0.465)	info on Rv0075/-
Rv2265/-	(cc=0.4649)	info on Rv2265/-

Correlation of Rv3892c/PPE69 with Rv1468c/PE_PGRS29

Normalized LFCs for Rv3892c/PPE69:
(description and provenance of datasets)

	Rv3892c/PPE69	Rv1468c/PE_PGRS29
Fe_supp_jason_reseq	0.262	0.425
low_pH_jason_reseq	-0.467	0.274
NO_jason_reseq	-1.601	-1.229
B6_jason_reseq	0.094	-0.718
MHCII_jason_reseq	-0.108	-0.801
Isoniazid02	2.267	0.303
Rifampicin4	0.723	1.968
Ethambutol3	2.274	1.278
Meropenem3	-0.126	1.473
Vancomycin16	0.058	0.43
Rv2680_day32	-1.335	-0.64
H37Rv_KO_MarP	0.555	-0.049
hypoxia_3wks	-0.658	-0.694
hypoxia_6wks	-0.912	-0.735
glycerol	0.257	0.0
cholesterol	0.441	-0.388
AJ	1.385	1.612
Bibs02	0.911	0.389
Bibs02c	0.453	0.0
BL6	-0.247	-0.835
BL6a	0.143	0.0
BXD01	-0.973	0.235
BXD010	-0.253	-0.675
BXD011	-0.23	-0.078
BXD03	0.108	-0.2
BXD04	0.019	0.024
BXD05	-0.161	0.308
BXD06	-1.104	-0.428
BXD07	-0.781	0.339
BXD08	0.288	0.519
BXD09	-0.331	0.054
CAST	1.049	0.415
CCcont	-0.578	0.168
DS01	0.898	0.652
DS02	1.054	0.789
DS04	1.703	1.835
DS0c	1.092	-0.178
GP01	0.3	1.93
GP02	0.482	0.863
GP0c	-0.222	1.155
NOD	0.083	-0.436
NZO	0.159	0.751
PWK	0.196	0.254
H37Rv_KO_CtpC	0.107	1.094
H37Rv_KO_CtpD	0.32	2.032
H37Rv_KO_Rv1272	0.774	1.204
H37Rv_KO_SugABC	-0.474	0.346
H37Rv_KO_MbtN	-0.023	1.692
Trans05	0.449	-0.193
macrophage_unactivated	-1.449	-0.117
IL1	0.341	-0.169
Rapamycin	-0.068	-0.608
Tcell	-0.45	0.059
GMCSF	0.058	0.143
IFNab	-0.345	-0.599
IFNg	-0.029	-1.141
IFNg_GMCSF1	-0.321	0.798
Rv1432_day32	-0.107	0.07
Rv1565c_day32	-0.959	-1.33
secA2_input	0.653	-0.462
delta_Rv3594	-0.291	0.6
delta_Rv3717	0.283	0.865
delta_Rv3811	-0.269	0.708
delta_Rv0954	0.77	1.499
PonA1	-0.241	0.99
EccD1_KO	-0.372	-0.523
EspI_KO	-0.414	-0.787
PE35_KO	-0.764	-0.505
PPE68_KO	-0.214	-0.291
glycerol2	0.412	-0.22
lignocerate	0.06	0.033
oleate	0.597	0.057
phosphatidylcholine	0.069	-0.262
acetate	0.02	-0.163
glucAc	-0.762	-0.491
Rv0950ko	-0.106	0.202
Rv1096ko	0.0	-0.127
Rv3684ko	-0.609	0.177
delta_otsA_trehalose	1.319	0.284