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 Rv0572c/-:

update plot	correlation	link to info on gene
Rv0443/-	(cc=0.5626)	info on Rv0443/-
Rv3742c/-	(cc=0.5123)	info on Rv3742c/-
Rv2777c/-	(cc=0.5088)	info on Rv2777c/-
Rv2689c/-	(cc=0.5066)	info on Rv2689c/-
Rv3555c/-	(cc=0.4841)	info on Rv3555c/-
Rv1087/PE_PGRS21	(cc=0.4734)	info on Rv1087/PE_PGRS21
Rv3738c/PPE66	(cc=0.4718)	info on Rv3738c/PPE66
Rv1604/impA	(cc=0.4639)	info on Rv1604/impA
Rv3287c/rsbW	(cc=0.4552)	info on Rv3287c/rsbW
Rv2892c/PPE45	(cc=0.4528)	info on Rv2892c/PPE45

Correlation of Rv0572c/- with Rv1087/PE_PGRS21

Normalized LFCs for Rv0572c/-:
(description and provenance of datasets)

	Rv0572c/-	Rv1087/PE_PGRS21
Fe_supp_jason_reseq	-0.704	-1.443
low_pH_jason_reseq	-0.642	-1.295
NO_jason_reseq	-0.113	-0.431
B6_jason_reseq	-0.323	-0.404
MHCII_jason_reseq	-0.164	-0.066
Isoniazid02	-0.442	-1.653
Rifampicin4	0.195	0.214
Ethambutol3	0.112	0.196
Meropenem3	-0.071	-0.639
Vancomycin16	0.082	-0.865
Rv2680_day32	-0.024	0.842
H37Rv_KO_MarP	-0.349	0.162
hypoxia_3wks	0.02	-0.427
hypoxia_6wks	0.52	-0.727
glycerol	0.786	1.262
cholesterol	0.303	0.519
AJ	-0.501	1.155
Bibs02	1.257	0.782
Bibs02c	0.668	0.838
BL6	0.552	0.186
BL6a	0.402	0.133
BXD01	-0.145	0.1
BXD010	0.242	0.2
BXD011	0.82	-0.79
BXD03	0.888	0.235
BXD04	0.015	-0.487
BXD05	0.184	-0.492
BXD06	0.319	0.014
BXD07	0.434	-0.43
BXD08	0.233	-0.431
BXD09	0.017	-0.437
CAST	0.047	-0.215
CCcont	0.799	-0.173
DS01	-0.284	-0.072
DS02	-0.08	0.414
DS04	0.055	0.777
DS0c	-0.036	-0.11
GP01	0.362	1.227
GP02	2.156	1.357
GP0c	0.117	0.136
NOD	0.063	0.944
NZO	0.032	-0.144
PWK	0.047	0.358
H37Rv_KO_CtpC	1.011	-0.461
H37Rv_KO_CtpD	0.638	1.767
H37Rv_KO_Rv1272	0.674	0.546
H37Rv_KO_SugABC	0.184	0.362
H37Rv_KO_MbtN	-0.143	0.196
Trans05	0.783	0.323
macrophage_unactivated	0.338	-0.919
IL1	-0.255	-2.441
Rapamycin	-0.071	-2.734
Tcell	-0.046	-1.825
GMCSF	-0.074	-0.935
IFNab	-0.348	-2.839
IFNg	-0.216	-1.497
IFNg_GMCSF1	-0.27	-2.061
Rv1432_day32	-0.229	0.568
Rv1565c_day32	0.662	-1.084
secA2_input	0.008	-0.551
delta_Rv3594	-0.184	0.095
delta_Rv3717	-0.034	-0.109
delta_Rv3811	0.039	-0.254
delta_Rv0954	-0.421	-1.503
PonA1	-0.517	-0.04
EccD1_KO	-0.056	-0.023
EspI_KO	0.482	-0.06
PE35_KO	-0.23	0.219
PPE68_KO	-0.237	-0.138
glycerol2	0.902	0.933
lignocerate	1.179	1.382
oleate	0.103	0.366
phosphatidylcholine	0.852	0.933
acetate	0.071	1.235
glucAc	0.395	1.491
Rv0950ko	0.063	0.289
Rv1096ko	0.763	0.878
Rv3684ko	0.331	0.57
delta_otsA_trehalose	2.429	1.004