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 Rv1396c/PE_PGRS25:

update plot	correlation	link to info on gene
Rv3115/-	(cc=0.6254)	info on Rv3115/-
Rv2479c/-	(cc=0.6214)	info on Rv2479c/-
Rv2512c/-	(cc=0.6208)	info on Rv2512c/-
Rv2106/-	(cc=0.6207)	info on Rv2106/-
Rv2814c/-	(cc=0.6204)	info on Rv2814c/-
Rv3475/-	(cc=0.6189)	info on Rv3475/-
Rv1047/-	(cc=0.6106)	info on Rv1047/-
Rv2279/-	(cc=0.6061)	info on Rv2279/-
Rv1369c/-	(cc=0.6048)	info on Rv1369c/-
Rv1756c/-	(cc=0.6034)	info on Rv1756c/-

Correlation of Rv1396c/PE_PGRS25 with Rv1756c/-

Normalized LFCs for Rv1396c/PE_PGRS25:
(description and provenance of datasets)

	Rv1396c/PE_PGRS25	Rv1756c/-
Fe_supp_jason_reseq	-1.14	-0.357
low_pH_jason_reseq	-0.545	-0.494
NO_jason_reseq	-1.701	0.362
B6_jason_reseq	-1.043	-0.418
MHCII_jason_reseq	-0.633	-0.043
Isoniazid02	-1.352	-0.102
Rifampicin4	0.921	0.915
Ethambutol3	-0.045	0.465
Meropenem3	-1.155	-0.223
Vancomycin16	-0.249	-0.239
Rv2680_day32	-0.48	0.281
H37Rv_KO_MarP	0.161	-0.199
hypoxia_3wks	-0.116	0.471
hypoxia_6wks	-0.896	0.067
glycerol	1.369	-0.295
cholesterol	1.175	0.336
AJ	2.575	1.632
Bibs02	1.734	1.44
Bibs02c	1.585	1.995
BL6	0.257	0.357
BL6a	0.809	1.422
BXD01	0.987	0.948
BXD010	0.562	1.088
BXD011	0.419	1.055
BXD03	0.352	1.007
BXD04	0.486	0.786
BXD05	0.975	1.323
BXD06	-0.463	0.75
BXD07	0.818	1.036
BXD08	1.008	0.632
BXD09	0.919	1.052
CAST	0.941	1.653
CCcont	0.515	0.279
DS01	0.395	1.261
DS02	0.821	1.215
DS04	0.325	1.502
DS0c	0.234	1.549
GP01	0.89	1.488
GP02	1.607	1.55
GP0c	1.185	1.012
NOD	0.0	1.565
NZO	0.905	1.376
PWK	0.831	1.582
H37Rv_KO_CtpC	1.369	1.007
H37Rv_KO_CtpD	2.165	1.03
H37Rv_KO_Rv1272	0.834	0.639
H37Rv_KO_SugABC	0.845	0.982
H37Rv_KO_MbtN	1.015	0.821
Trans05	0.408	1.029
macrophage_unactivated	-0.145	-0.821
IL1	-0.089	-0.641
Rapamycin	-1.034	-0.77
Tcell	0.0	-1.499
GMCSF	-0.121	-0.393
IFNab	-0.429	-1.094
IFNg	-0.901	-0.556
IFNg_GMCSF1	0.138	-0.339
Rv1432_day32	0.553	0.587
Rv1565c_day32	0.257	0.262
secA2_input	-0.601	0.016
delta_Rv3594	1.319	-0.15
delta_Rv3717	0.32	-0.243
delta_Rv3811	0.697	-0.201
delta_Rv0954	-0.092	0.544
PonA1	0.21	-0.07
EccD1_KO	0.303	0.661
EspI_KO	1.3	0.858
PE35_KO	0.933	0.645
PPE68_KO	0.403	0.666
glycerol2	-0.479	-1.131
lignocerate	-0.897	-0.884
oleate	0.465	-1.304
phosphatidylcholine	-0.342	-1.098
acetate	0.0	-0.239
glucAc	-0.734	0.007
Rv0950ko	-0.437	-0.142
Rv1096ko	-1.644	0.115
Rv3684ko	-0.416	-0.727
delta_otsA_trehalose	-0.525	0.329