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 Rv3509c/ilvX:

update plot	correlation	link to info on gene
Rv0578c/PE_PGRS7	(cc=0.6284)	info on Rv0578c/PE_PGRS7
Rv0218/-	(cc=0.5765)	info on Rv0218/-
Rv3624c/hpt	(cc=0.5668)	info on Rv3624c/hpt
Rv3344c/PE_PGRS49	(cc=0.5628)	info on Rv3344c/PE_PGRS49
Rv2841c/nusA	(cc=0.5514)	info on Rv2841c/nusA
Rv1135c/PPE16	(cc=0.5487)	info on Rv1135c/PPE16
Rv3607c/folB	(cc=0.5436)	info on Rv3607c/folB
Rv0835/lpqQ	(cc=0.5344)	info on Rv0835/lpqQ
Rv1734c/-	(cc=0.5338)	info on Rv1734c/-
Rv2571c/-	(cc=0.5323)	info on Rv2571c/-

Correlation of Rv3509c/ilvX with Rv1135c/PPE16

Normalized LFCs for Rv3509c/ilvX:
(description and provenance of datasets)

	Rv3509c/ilvX	Rv1135c/PPE16
Fe_supp_jason_reseq	-0.081	-0.655
low_pH_jason_reseq	-0.375	-1.094
NO_jason_reseq	-0.257	-0.551
B6_jason_reseq	0.367	-0.13
MHCII_jason_reseq	0.362	0.093
Isoniazid02	1.147	0.362
Rifampicin4	0.55	1.075
Ethambutol3	0.899	0.67
Meropenem3	0.328	0.718
Vancomycin16	0.727	0.846
Rv2680_day32	-0.207	-0.104
H37Rv_KO_MarP	0.302	-0.344
hypoxia_3wks	-0.104	-0.65
hypoxia_6wks	-0.355	-0.443
glycerol	0.699	0.151
cholesterol	0.869	0.101
AJ	0.282	0.402
Bibs02	0.34	0.646
Bibs02c	0.45	0.382
BL6	0.502	-0.562
BL6a	0.458	-0.37
BXD01	0.516	-0.218
BXD010	0.03	-0.642
BXD011	0.68	-0.181
BXD03	0.047	-0.455
BXD04	0.408	-0.192
BXD05	-0.064	0.289
BXD06	0.39	-0.469
BXD07	0.174	-0.111
BXD08	-0.011	-0.267
BXD09	0.126	-0.472
CAST	0.207	-0.103
CCcont	-0.281	-1.193
DS01	0.409	0.26
DS02	0.28	0.365
DS04	0.835	0.916
DS0c	0.594	0.456
GP01	-0.119	-1.134
GP02	-0.02	0.087
GP0c	-0.314	-0.64
NOD	0.714	0.202
NZO	-0.048	-0.373
PWK	0.415	0.429
H37Rv_KO_CtpC	-0.006	0.187
H37Rv_KO_CtpD	0.044	0.473
H37Rv_KO_Rv1272	0.167	0.315
H37Rv_KO_SugABC	0.471	-0.288
H37Rv_KO_MbtN	0.257	0.098
Trans05	0.094	0.446
macrophage_unactivated	-0.732	-0.48
IL1	-0.602	-1.017
Rapamycin	-0.868	-0.644
Tcell	-0.459	-0.111
GMCSF	-0.428	-0.528
IFNab	-0.856	-0.91
IFNg	-0.877	-1.28
IFNg_GMCSF1	0.226	-0.305
Rv1432_day32	0.756	0.343
Rv1565c_day32	0.175	0.253
secA2_input	-0.189	-0.437
delta_Rv3594	0.783	0.395
delta_Rv3717	0.039	0.257
delta_Rv3811	0.651	0.031
delta_Rv0954	0.915	0.72
PonA1	0.743	0.128
EccD1_KO	0.072	0.658
EspI_KO	-0.125	0.456
PE35_KO	-0.064	0.939
PPE68_KO	-0.384	0.761
glycerol2	-0.174	-0.566
lignocerate	-0.358	-0.252
oleate	-0.33	-0.313
phosphatidylcholine	-0.209	-0.115
acetate	-0.849	-0.411
glucAc	-0.171	-0.255
Rv0950ko	0.612	-0.211
Rv1096ko	0.953	-0.211
Rv3684ko	0.4	-0.783
delta_otsA_trehalose	-0.209	-0.926