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 Rv2088/pknJ:

update plot	correlation	link to info on gene
Rv0833/PE_PGRS13	(cc=0.5203)	info on Rv0833/PE_PGRS13
Rv1728c/-	(cc=0.4917)	info on Rv1728c/-
Rv1452c/PE_PGRS28	(cc=0.4782)	info on Rv1452c/PE_PGRS28
Rv3513c/fadD18	(cc=0.4742)	info on Rv3513c/fadD18
Rv2022c/-	(cc=0.4738)	info on Rv2022c/-
Rv3144c/PPE52	(cc=0.4645)	info on Rv3144c/PPE52
Rv1781c/malQ	(cc=0.4592)	info on Rv1781c/malQ
Rv1245c/-	(cc=0.4545)	info on Rv1245c/-
Rv3507/PE_PGRS53	(cc=0.4533)	info on Rv3507/PE_PGRS53
Rv1004c/-	(cc=0.453)	info on Rv1004c/-

Correlation of Rv2088/pknJ with Rv3513c/fadD18

Normalized LFCs for Rv2088/pknJ:
(description and provenance of datasets)

	Rv2088/pknJ	Rv3513c/fadD18
Fe_supp_jason_reseq	-0.822	0.587
low_pH_jason_reseq	0.0	-1.405
NO_jason_reseq	-0.32	-0.641
B6_jason_reseq	-0.171	-0.099
MHCII_jason_reseq	0.479	0.442
Isoniazid02	-0.02	0.064
Rifampicin4	0.463	0.219
Ethambutol3	-0.179	-0.258
Meropenem3	0.307	-0.527
Vancomycin16	0.584	-0.446
Rv2680_day32	0.407	0.057
H37Rv_KO_MarP	-0.522	0.079
hypoxia_3wks	0.73	0.267
hypoxia_6wks	-0.255	0.161
glycerol	0.206	-0.006
cholesterol	0.233	-0.232
AJ	0.237	0.509
Bibs02	-0.101	-0.037
Bibs02c	0.905	0.23
BL6	-0.555	-0.222
BL6a	0.386	-0.011
BXD01	-0.187	-0.413
BXD010	0.083	-0.272
BXD011	-0.07	0.209
BXD03	-0.036	0.459
BXD04	-0.033	-0.215
BXD05	0.201	0.248
BXD06	0.275	-0.131
BXD07	0.285	-0.27
BXD08	-0.512	-0.292
BXD09	0.193	0.029
CAST	0.782	0.272
CCcont	-0.757	-0.516
DS01	-0.339	0.087
DS02	-0.345	0.153
DS04	0.659	0.333
DS0c	0.113	0.467
GP01	0.735	0.36
GP02	1.395	0.4
GP0c	0.209	0.223
NOD	0.807	-0.285
NZO	-0.166	0.178
PWK	0.0	0.728
H37Rv_KO_CtpC	-0.022	0.028
H37Rv_KO_CtpD	0.829	0.961
H37Rv_KO_Rv1272	0.841	0.155
H37Rv_KO_SugABC	1.222	0.873
H37Rv_KO_MbtN	-0.458	0.055
Trans05	0.698	0.116
macrophage_unactivated	-0.514	-0.243
IL1	-0.116	-0.303
Rapamycin	-0.632	-0.5
Tcell	-0.531	-0.531
GMCSF	0.246	0.042
IFNab	-0.302	-0.109
IFNg	-0.104	-0.388
IFNg_GMCSF1	0.06	0.17
Rv1432_day32	0.559	-0.33
Rv1565c_day32	-0.09	0.34
secA2_input	-1.257	-0.149
delta_Rv3594	0.635	-0.006
delta_Rv3717	0.341	0.118
delta_Rv3811	0.287	-0.031
delta_Rv0954	-0.394	-0.119
PonA1	0.223	0.367
EccD1_KO	-0.51	-0.293
EspI_KO	-0.171	-0.405
PE35_KO	-0.044	-0.108
PPE68_KO	-0.048	-0.685
glycerol2	-0.09	0.205
lignocerate	-0.407	0.101
oleate	0.384	0.366
phosphatidylcholine	0.0	0.22
acetate	-0.427	-0.191
glucAc	-0.823	-0.026
Rv0950ko	0.326	1.019
Rv1096ko	0.953	0.464
Rv3684ko	0.403	0.802
delta_otsA_trehalose	-1.715	-1.296