analysis/01.SelectGenes/Markers_1.1/comparison_CellTypes-Markers_1.0-Markers_1.1.md
In oganm/brainGenesManuscript: Marker genes of brain cell types and their use in analysis of whole tissue data
All
Astrocyte
Total gene count: 97
removed (1): Pdgfc
added (2): Sox9, Vegfa
Microglia
Total gene count: 131
removed (2): Clic1, Srgap2
Microglia_activation
Total gene count: 96
removed (2): Gbp7, Slc39a8
added (1): Igtp
Microglia_deactivation
Total gene count: 109
added (2): Prkcd, Samhd1
Noradrenergic
Total gene count: 9
removed (2): Gstm6, Stbd1
Oligo
Total gene count: 23
removed (1): Lpar1
Amygdala
Astrocyte
Total gene count: 150
removed (1): Adgrg1
added (2): Sorcs2, Vegfa
Microglia
Total gene count: 150
added (1): Skap2
Microglia_deactivation
Total gene count: 146
removed (1): Scamp2
added (4): Cd2ap, Man2b1, Ppfia4, Tmcc3
BasalForebrain
Astrocyte
Total gene count: 149
removed (1): Add3
added (2): Notch1, Sox9
ForebrainCholin
Total gene count: 93
added (2): Hs6st2, Nipsnap1
Microglia
Total gene count: 156
removed (1): Gns
added (1): Ptprj
Microglia_deactivation
Total gene count: 136
added (1): Ppfia4
Brainstem
Astrocyte
Total gene count: 139
removed (2): Aqp4, Pdk4
added (1): Sox21
BrainstemCholin
Total gene count: 29
removed (1): Hspb8
Microglia
Total gene count: 154
added (3): Adamts1, Dusp6, Ptprj
Microglia_activation
Total gene count: 107
removed (1): Il4ra
Microglia_deactivation
Total gene count: 142
added (2): Fosb, Ppfia4
Noradrenergic
Total gene count: 17
added (1): Gstm6
Cerebellum
Basket
Total gene count: 7
removed (1): Cidea
added (1): Parm1
Bergmann
Total gene count: 59
removed (2): Aard, Calml4
added (8): Acsbg1, Cxcl14, Fgfr3, Gjb6, Gramd3, Mfge8, Pltp, Rab34
CerebGranule
Total gene count: 5
removed (5): Calb2, Car4, Dleu2, Eomes, Tesc
Golgi
Total gene count: 28
removed (1): Kcnmb2
added (4): 2010204K13Rik, C1ql3, Cplx3, Rgs6
Microglia
Total gene count: 189
removed (3): Cttnbp2nl, Myh9, Skap2
added (11): Abcg2, Adam17, Apobec1, BC028528, Casp7, Epb41l2, Parp12, Ptprj, Ssfa2, Stt3a, Syngr2
Microglia_activation
Total gene count: 127
added (4): Arpc1b, Cd164, Ptk2b, Rsad2
Microglia_deactivation
Total gene count: 163
added (4): Mmp2, Pdk1, Ppfia4, Sox4
Oligo
Total gene count: 51
removed (2): Gal3st1, Jam3
added (14): Apod, Enpp4, Fbxo32, Gjc3, Gstm7, Il33, Kctd4, Klk6, Nfe2l3, Pcolce2, Rapgef3, Serpinb1a, St6galnac3, Tnfaip6
Purkinje
Total gene count: 44
removed (1): Calb1
added (2): Igf1, Pcp2
Cerebrum
Astrocyte
Total gene count: 176
removed (2): Cyp2j6, Id3
DentateGranule
Total gene count: 12
added (1): Ccdc85a
Microglia
Total gene count: 174
removed (1): Ctsz
added (1): Mef2a
Microglia_deactivation
Total gene count: 148
added (1): Ppfia4
Oligo
Total gene count: 48
added (1): Thbs3
Cortex
Astrocyte
Total gene count: 302
removed (1): 2810459M11Rik
added (1): Rorb
GabaPV
Total gene count: 26
removed (1): Gpr83
GabaRelnCalb
Total gene count: 23
added (1): Moxd1
GabaVIPReln
Total gene count: 47
added (1): Pcdhb14
Microglia_deactivation
Total gene count: 206
removed (2): Ndst2, Snx29
Oligo
Total gene count: 164
removed (1): Fign
added (1): Scd2
Hippocampus
Astrocyte
Total gene count: 138
removed (3): Agl, Cspg5, Dtna
added (1): Sox9
GabaSSTReln
Total gene count: 55
added (1): Pcsk1
Microglia
Total gene count: 154
removed (1): Gns
Microglia_activation
Total gene count: 111
removed (1): Atp7a
Microglia_deactivation
Total gene count: 137
added (1): Ppfia4
Oligo
Total gene count: 49
removed (1): Tnni1
LocusCoeruleus
Astrocyte
Total gene count: 139
removed (3): Acaa2, Notch1, Sox9
Microglia
Total gene count: 149
added (2): Myo1b, Ptprj
Microglia_activation
Total gene count: 105
removed (1): Plaur
Microglia_deactivation
Total gene count: 139
added (1): Ppfia4
Noradrenergic
Total gene count: 134
removed (2): Dmtn, Dync1i1
added (1): H13
Oligo
Total gene count: 53
removed (1): Tmeff2
Midbrain
Astrocyte
Total gene count: 128
removed (1): Bcan
added (2): Crot, Tmem51
BrainstemCholin
Total gene count: 35
added (1): Nefh
Microglia
Total gene count: 153
removed (1): Tgif2
Microglia_deactivation
Total gene count: 138
added (2): Ppfia4, Slc7a8
Oligo
Total gene count: 19
added (1): Aspa
SpinalCord
Astrocyte
Total gene count: 140
added (2): Fxyd1, Itsn1
Microglia
Total gene count: 149
added (2): Emp3, Ptprj
Microglia_activation
Total gene count: 103
removed (1): Atp7a
Microglia_deactivation
Total gene count: 136
added (2): Lst1, Ppfia4
SpinalCordCholinergic
Total gene count: 126
added (1): Syt4
Striatum
Astrocyte
Total gene count: 193
removed (2): Lrp4, Metrn
added (1): Rdh5
ForebrainCholin
Total gene count: 45
added (2): Stmn2, Unc119
Microglia
Total gene count: 168
removed (3): Cklf, Rin2, Spata13
Microglia_activation
Total gene count: 114
removed (1): Gbp7
Microglia_deactivation
Total gene count: 146
removed (1): Ptpre
added (1): Ppfia4
Oligo
Total gene count: 52
removed (2): Cdc42ep1, Ninj2
Spiny
Total gene count: 72
removed (2): Arpp21, Cap2
added (1): D430019H16Rik
Subependymal
Astrocyte
Total gene count: 112
removed (1): Emp2
Ependymal
Total gene count: 48
added (1): Top2a
Microglia
Total gene count: 114
added (2): B2m, Ptprj
Microglia_deactivation
Total gene count: 102
removed (3): Lst1, Naip6, Pycard
added (1): Ppfia4
Oligo
Total gene count: 53
removed (1): Wfdc18
SubstantiaNigra
Astrocyte
Total gene count: 96
removed (2): Notch1, Trps1
added (2): Axl, Rorb
Dopaminergic
Total gene count: 58
removed (2): Gria3, Syp
added (1): Cers4
Microglia
Total gene count: 145
removed (1): B2m
Microglia_activation
Total gene count: 95
added (1): Tlr6
Microglia_deactivation
Total gene count: 128
removed (1): Lst1
added (1): Ppfia4
Oligo
Total gene count: 18
added (1): Tspan2
Thalamus
Astrocyte
Total gene count: 160
removed (1): Sox9
added (1): Fbln1
Microglia
Total gene count: 158
added (2): Cklf, Ptprj
Microglia_deactivation
Total gene count: 137
removed (2): Naip6, Rbl1
oganm/brainGenesManuscript documentation built on Aug. 24, 2022, 7:48 p.m.
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All
Astrocyte
Total gene count: 97
removed (1): Pdgfc
added (2): Sox9, Vegfa
Microglia
Total gene count: 131
removed (2): Clic1, Srgap2
Microglia_activation
Total gene count: 96
removed (2): Gbp7, Slc39a8
added (1): Igtp
Microglia_deactivation
Total gene count: 109
added (2): Prkcd, Samhd1
Noradrenergic
Total gene count: 9
removed (2): Gstm6, Stbd1
Oligo
Total gene count: 23
removed (1): Lpar1
Amygdala
Astrocyte
Total gene count: 150
removed (1): Adgrg1
added (2): Sorcs2, Vegfa
Microglia
Total gene count: 150
added (1): Skap2
Microglia_deactivation
Total gene count: 146
removed (1): Scamp2
added (4): Cd2ap, Man2b1, Ppfia4, Tmcc3
BasalForebrain
Astrocyte
Total gene count: 149
removed (1): Add3
added (2): Notch1, Sox9
ForebrainCholin
Total gene count: 93
added (2): Hs6st2, Nipsnap1
Microglia
Total gene count: 156
removed (1): Gns
added (1): Ptprj
Microglia_deactivation
Total gene count: 136
added (1): Ppfia4
Brainstem
Astrocyte
Total gene count: 139
removed (2): Aqp4, Pdk4
added (1): Sox21
BrainstemCholin
Total gene count: 29
removed (1): Hspb8
Microglia
Total gene count: 154
added (3): Adamts1, Dusp6, Ptprj
Microglia_activation
Total gene count: 107
removed (1): Il4ra
Microglia_deactivation
Total gene count: 142
added (2): Fosb, Ppfia4
Noradrenergic
Total gene count: 17
added (1): Gstm6
Cerebellum
Basket
Total gene count: 7
removed (1): Cidea
added (1): Parm1
Bergmann
Total gene count: 59
removed (2): Aard, Calml4
added (8): Acsbg1, Cxcl14, Fgfr3, Gjb6, Gramd3, Mfge8, Pltp, Rab34
CerebGranule
Total gene count: 5
removed (5): Calb2, Car4, Dleu2, Eomes, Tesc
Golgi
Total gene count: 28
removed (1): Kcnmb2
added (4): 2010204K13Rik, C1ql3, Cplx3, Rgs6
Microglia
Total gene count: 189
removed (3): Cttnbp2nl, Myh9, Skap2
added (11): Abcg2, Adam17, Apobec1, BC028528, Casp7, Epb41l2, Parp12, Ptprj, Ssfa2, Stt3a, Syngr2
Microglia_activation
Total gene count: 127
added (4): Arpc1b, Cd164, Ptk2b, Rsad2
Microglia_deactivation
Total gene count: 163
added (4): Mmp2, Pdk1, Ppfia4, Sox4
Oligo
Total gene count: 51
removed (2): Gal3st1, Jam3
added (14): Apod, Enpp4, Fbxo32, Gjc3, Gstm7, Il33, Kctd4, Klk6, Nfe2l3, Pcolce2, Rapgef3, Serpinb1a, St6galnac3, Tnfaip6
Purkinje
Total gene count: 44
removed (1): Calb1
added (2): Igf1, Pcp2
Cerebrum
Astrocyte
Total gene count: 176
removed (2): Cyp2j6, Id3
DentateGranule
Total gene count: 12
added (1): Ccdc85a
Microglia
Total gene count: 174
removed (1): Ctsz
added (1): Mef2a
Microglia_deactivation
Total gene count: 148
added (1): Ppfia4
Oligo
Total gene count: 48
added (1): Thbs3
Cortex
Astrocyte
Total gene count: 302
removed (1): 2810459M11Rik
added (1): Rorb
GabaPV
Total gene count: 26
removed (1): Gpr83
GabaRelnCalb
Total gene count: 23
added (1): Moxd1
GabaVIPReln
Total gene count: 47
added (1): Pcdhb14
Microglia_deactivation
Total gene count: 206
removed (2): Ndst2, Snx29
Oligo
Total gene count: 164
removed (1): Fign
added (1): Scd2
Hippocampus
Astrocyte
Total gene count: 138
removed (3): Agl, Cspg5, Dtna
added (1): Sox9
GabaSSTReln
Total gene count: 55
added (1): Pcsk1
Microglia
Total gene count: 154
removed (1): Gns
Microglia_activation
Total gene count: 111
removed (1): Atp7a
Microglia_deactivation
Total gene count: 137
added (1): Ppfia4
Oligo
Total gene count: 49
removed (1): Tnni1
LocusCoeruleus
Astrocyte
Total gene count: 139
removed (3): Acaa2, Notch1, Sox9
Microglia
Total gene count: 149
added (2): Myo1b, Ptprj
Microglia_activation
Total gene count: 105
removed (1): Plaur
Microglia_deactivation
Total gene count: 139
added (1): Ppfia4
Noradrenergic
Total gene count: 134
removed (2): Dmtn, Dync1i1
added (1): H13
Oligo
Total gene count: 53
removed (1): Tmeff2
Midbrain
Astrocyte
Total gene count: 128
removed (1): Bcan
added (2): Crot, Tmem51
BrainstemCholin
Total gene count: 35
added (1): Nefh
Microglia
Total gene count: 153
removed (1): Tgif2
Microglia_deactivation
Total gene count: 138
added (2): Ppfia4, Slc7a8
Oligo
Total gene count: 19
added (1): Aspa
SpinalCord
Astrocyte
Total gene count: 140
added (2): Fxyd1, Itsn1
Microglia
Total gene count: 149
added (2): Emp3, Ptprj
Microglia_activation
Total gene count: 103
removed (1): Atp7a
Microglia_deactivation
Total gene count: 136
added (2): Lst1, Ppfia4
SpinalCordCholinergic
Total gene count: 126
added (1): Syt4
Striatum
Astrocyte
Total gene count: 193
removed (2): Lrp4, Metrn
added (1): Rdh5
ForebrainCholin
Total gene count: 45
added (2): Stmn2, Unc119
Microglia
Total gene count: 168
removed (3): Cklf, Rin2, Spata13
Microglia_activation
Total gene count: 114
removed (1): Gbp7
Microglia_deactivation
Total gene count: 146
removed (1): Ptpre
added (1): Ppfia4
Oligo
Total gene count: 52
removed (2): Cdc42ep1, Ninj2
Spiny
Total gene count: 72
removed (2): Arpp21, Cap2
added (1): D430019H16Rik
Subependymal
Astrocyte
Total gene count: 112
removed (1): Emp2
Ependymal
Total gene count: 48
added (1): Top2a
Microglia
Total gene count: 114
added (2): B2m, Ptprj
Microglia_deactivation
Total gene count: 102
removed (3): Lst1, Naip6, Pycard
added (1): Ppfia4
Oligo
Total gene count: 53
removed (1): Wfdc18
SubstantiaNigra
Astrocyte
Total gene count: 96
removed (2): Notch1, Trps1
added (2): Axl, Rorb
Dopaminergic
Total gene count: 58
removed (2): Gria3, Syp
added (1): Cers4
Microglia
Total gene count: 145
removed (1): B2m
Microglia_activation
Total gene count: 95
added (1): Tlr6
Microglia_deactivation
Total gene count: 128
removed (1): Lst1
added (1): Ppfia4
Oligo
Total gene count: 18
added (1): Tspan2
Thalamus
Astrocyte
Total gene count: 160
removed (1): Sox9
added (1): Fbln1
Microglia
Total gene count: 158
added (2): Cklf, Ptprj
Microglia_deactivation
Total gene count: 137
removed (2): Naip6, Rbl1
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