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 Rv1067c/PE_PGRS19:

update plot	correlation	link to info on gene
Rv0578c/PE_PGRS7	(cc=0.5722)	info on Rv0578c/PE_PGRS7
Rv1091/PE_PGRS22	(cc=0.5702)	info on Rv1091/PE_PGRS22
Rv1452c/PE_PGRS28	(cc=0.5443)	info on Rv1452c/PE_PGRS28
Rv0526/-	(cc=0.5346)	info on Rv0526/-
Rv3533c/PPE62	(cc=0.5314)	info on Rv3533c/PPE62
Rv3022A/PE29	(cc=0.5123)	info on Rv3022A/PE29
Rv1709/scpA	(cc=0.4986)	info on Rv1709/scpA
Rv1756c/-	(cc=0.4911)	info on Rv1756c/-
Rv0598c/vapC27	(cc=0.4799)	info on Rv0598c/vapC27
Rv2228c/-	(cc=0.474)	info on Rv2228c/-

Correlation of Rv1067c/PE_PGRS19 with Rv3022A/PE29

Normalized LFCs for Rv1067c/PE_PGRS19:
(description and provenance of datasets)

	Rv1067c/PE_PGRS19	Rv3022A/PE29
Fe_supp_jason_reseq	0.137	0.275
low_pH_jason_reseq	-0.734	-0.381
NO_jason_reseq	-0.559	-0.709
B6_jason_reseq	-0.082	-0.585
MHCII_jason_reseq	-0.054	-0.709
Isoniazid02	-0.706	0.994
Rifampicin4	-0.087	0.967
Ethambutol3	-0.019	0.434
Meropenem3	1.429	0.291
Vancomycin16	-0.589	0.594
Rv2680_day32	-0.223	-0.826
H37Rv_KO_MarP	-0.133	0.165
hypoxia_3wks	-0.056	0.347
hypoxia_6wks	-0.589	-0.81
glycerol	1.303	0.73
cholesterol	0.513	1.146
AJ	1.277	2.274
Bibs02	0.313	0.167
Bibs02c	0.474	0.893
BL6	-0.18	0.569
BL6a	-0.174	0.641
BXD01	0.78	0.898
BXD010	0.104	0.456
BXD011	-0.313	0.286
BXD03	-0.046	0.216
BXD04	-0.178	0.063
BXD05	-0.22	0.775
BXD06	0.407	0.593
BXD07	0.068	0.93
BXD08	0.471	0.28
BXD09	0.135	0.383
CAST	0.36	1.099
CCcont	0.025	1.022
DS01	0.154	0.883
DS02	0.521	0.745
DS04	0.386	0.748
DS0c	0.401	-0.019
GP01	1.139	0.72
GP02	1.098	0.311
GP0c	0.24	0.208
NOD	0.285	0.919
NZO	0.608	-0.088
PWK	0.128	0.494
H37Rv_KO_CtpC	0.454	1.553
H37Rv_KO_CtpD	0.874	1.287
H37Rv_KO_Rv1272	0.69	2.221
H37Rv_KO_SugABC	-0.034	0.898
H37Rv_KO_MbtN	-0.616	0.687
Trans05	-0.469	1.378
macrophage_unactivated	-0.117	0.767
IL1	-1.16	0.039
Rapamycin	-0.405	0.264
Tcell	-0.365	0.525
GMCSF	0.615	1.333
IFNab	-0.46	0.768
IFNg	-0.569	0.083
IFNg_GMCSF1	0.057	0.289
Rv1432_day32	0.428	0.85
Rv1565c_day32	-0.648	2.139
secA2_input	1.522	0.182
delta_Rv3594	-0.326	0.34
delta_Rv3717	-0.596	0.145
delta_Rv3811	-0.36	0.427
delta_Rv0954	-1.79	-0.225
PonA1	0.029	0.516
EccD1_KO	0.608	0.947
EspI_KO	0.034	1.178
PE35_KO	0.572	0.84
PPE68_KO	0.118	0.579
glycerol2	-1.886	-1.302
lignocerate	-1.465	-0.961
oleate	-0.8	-1.032
phosphatidylcholine	-1.335	-0.819
acetate	-1.682	-1.248
glucAc	-1.271	-0.722
Rv0950ko	0.208	0.555
Rv1096ko	0.238	-0.347
Rv3684ko	-0.17	-0.354
delta_otsA_trehalose	0.157	-1.531