Category

GOTERM_BP_FAT

Supplementary Table 2. GO analysis (downregulated genes)

GO term analysis was performed to identify biological processes enriched among genes downregulated after depletion of LIN9

Analysis with the DAVID programs

Term Count

GO:0022402~cell cycle process 30

GO:0000279~M phase 26

GO:0007049~cell cycle 34

GO:0000087~M phase of mitotic cell cycle 22

GO:0022403~cell cycle phase 26

GO:0000278~mitotic cell cycle 23

GO:0000280~nuclear division 21

GO:0007067~mitosis 21

GO:0048285~organelle fission 21

GO:0051301~cell division 21

GO:0007059~chromosome segregation 9

GO:0006323~DNA packaging 10

GO:0034622~cellular macromolecular complex assembly 12

GO:0006334~nucleosome assembly 8

GO:0031497~chromatin assembly 8

GO:0034728~nucleosome organization 8

GO:0065004~protein-DNA complex assembly 8

GO:0034621~cellular macromolecular complex subunit organization 12

GO:0065003~macromolecular complex assembly 13

GO:0006333~chromatin assembly or disassembly 8

GO:0051276~chromosome organization 14

GO:0043933~macromolecular complex subunit organization 13

GO:0051327~M phase of meiotic cell cycle 6

GO:0007126~meiosis 6

GO:0051321~meiotic cell cycle 6

GO:0006325~chromatin organization 10

GO:0000910~cytokinesis 4

GO:0007017~microtubule-based process 8

GO:0045132~meiotic chromosome segregation 3

GO:0006979~response to oxidative stress 5

GO:0007018~microtubule-based movement 5

GO:0051640~organelle localization 4

GO:0045664~regulation of neuron differentiation 5

GO:0060341~regulation of cellular localization 6

GO:0007050~cell cycle arrest 4

GO:0007263~nitric oxide mediated signal transduction 2

GO:0051651~maintenance of location in cell 3

GO:0001709~cell fate determination 3

GO:0009636~response to toxin 3

GO:0010273~detoxification of copper ion 2

GO:0045143~homologous chromosome segregation 2

GO:0050767~regulation of neurogenesis 5

GO:0001701~in utero embryonic development 7

GO:0051235~maintenance of location 3

GO:0045651~positive regulation of macrophage differentiation 2

GO:0060024~rhythmic synaptic transmission 2

GO:0045787~positive regulation of cell cycle 3

GO:0051726~regulation of cell cycle 6

GO:0051960~regulation of nervous system development 5

GO:0032880~regulation of protein localization 4

GO:0045649~regulation of macrophage differentiation 2

GO:0010035~response to inorganic substance 4

GO:0051258~protein polymerization 3

GO:0060284~regulation of cell development 5

GO:0007242~intracellular signaling cascade 14

GO:0007346~regulation of mitotic cell cycle 4

GO:0051240~positive regulation of multicellular organismal process 5

GO:0030900~forebrain development 5

GO:0021700~developmental maturation 4

GO:0032886~regulation of microtubule-based process 3

GO:0006882~cellular zinc ion homeostasis 2

GO:0046688~response to copper ion 2

GO:0043623~cellular protein complex assembly 4

GO:0055069~zinc ion homeostasis 2

GO:0000226~microtubule cytoskeleton organization 4

GO:0000075~cell cycle checkpoint 3

GO:0044265~cellular macromolecule catabolic process 10

GO:0042770~DNA damage response, signal transduction 3

GO:0051603~proteolysis involved in cellular protein catabolic process 9

GO:0044257~cellular protein catabolic process 9

GO:0045860~positive regulation of protein kinase activity 4

GO:0042403~thyroid hormone metabolic process 2

GO:0006468~protein amino acid phosphorylation 10

GO:0033674~positive regulation of kinase activity 4

Supplementary Table 2. GO analysis (downregulated genes)

GO term analysis was performed to identify biological processes enriched among genes downregulated after depletion of LIN9

% PValue

17.543859649 1.44E-19

15.204678363 8.88E-19

19.883040936 3.98E-18

12.865497076 1.11E-17

15.204678363 3.04E-17

13.450292398 8.80E-17

12.280701754 1.23E-16

12.280701754 2.50E-16

12.280701754 2.47E-13

5.2631578947 6.57E-08

5.8479532164 1.91E-07

7.0175438596 2.42E-06

4.6783625731 2.82E-06

4.6783625731 3.39E-06

4.6783625731 3.70E-06

7.0175438596 7.77E-06

7.6023391813 3.12E-05

4.6783625731 4.00E-05

8.1871345029 4.01E-05

7.6023391813 6.93E-05

3.5087719298 9.27E-04

3.5087719298 0.0010259148

5.8479532164 0.0015001113

2.3391812865 0.0015270822

4.6783625731 0.0022024653

1.7543859649 0.0037789423

2.9239766082 0.0065148668

2.9239766082 0.0109141901

2.3391812865 0.01096207

2.9239766082 0.0112864755

3.5087719298 0.0122767246

2.3391812865 0.0126955728

1.1695906433 0.0170016323

1.7543859649 0.0190707912

1.7543859649 0.0220677322

1.7543859649 0.0252456356

1.1695906433 0.02539467

2.9239766082 0.0264558848

4.0935672515 0.0268788076

1.7543859649 0.0321168771

1.1695906433 0.0337166588

1.7543859649 0.0339372113

3.5087719298 0.0364143664

2.9239766082 0.0379327122

2.3391812865 0.0416941342

1.1695906433 0.041968195

2.3391812865 0.0440333803

1.7543859649 0.0456589733

2.9239766082 0.0472465196

8.1871345029 0.0481236086

2.3391812865 0.0489043918

2.9239766082 0.0509216416

2.9239766082 0.0547497949

2.3391812865 0.0553479331

1.7543859649 0.0563911722

1.1695906433 0.0582622697

2.3391812865 0.0650122029

1.1695906433 0.0663059761

2.3391812865 0.0693767861

1.7543859649 0.0727096696

5.8479532164 0.0762979377

1.7543859649 0.085177936

5.2631578947 0.0864408265

5.2631578947 0.0885917885

2.3391812865 0.0897515092

1.1695906433 0.0900306772

5.8479532164 0.0965464993

2.3391812865 0.099909175

GO term analysis was performed to identify biological processes enriched among genes downregulated after depletion of LIN9

Genes

NM_001014976, NM_010436, NM_133851, NM_009791, NM_021515, NM_013917, NM_175384, NM_009876, NM_023223, NM_173762, NM_011121, NM_009774, NM_028222, NM_016692, NM_011496, NM_001081363, NM_010891, NM_007628, NM_007659, NM_009860, NM_001040435, NM_153058, NM_027975, NM_007634, NM_026785, NM_001079876, NM_001081117, NM_028232, NM_017407, NM_172301

NM_001014976, NM_010436, NM_133851, NM_009791, NM_013917, NM_175384, NM_011121, NM_023223, NM_173762, NM_009774, NM_016692, NM_011496, NM_001081363, NM_010891, NM_007628, NM_007659, NM_009860, NM_001040435, NM_027975, NM_007634, NM_153058, NM_026785, NM_001081117, NM_028232, NM_172301, NM_017407

NM_001014976, NM_010436, NM_016681, NM_133851, NM_009791, NM_001103182, NM_021515, NM_013917, NM_175384, NM_009876, NM_023223, NM_173762, NM_011121, NM_020572, NM_009774, NM_028222, NM_016692, NM_011496, NM_011497, NM_001081363, NM_010891, NM_007628, NM_007659, NM_009860, NM_001040435, NM_153058, NM_027975, NM_007634, NM_026785, NM_001079876, NM_001081117, NM_028232, NM_017407, NM_172301

NM_016692, NM_011496, NM_001081363, NM_010891, NM_133851, NM_007628, NM_009791, NM_007659, NM_009860, NM_175384, NM_013917, NM_011121, NM_153058, NM_027975, NM_173762, NM_023223, NM_007634, NM_026785, NM_009774, NM_028232, NM_017407, NM_172301

NM_001014976, NM_010436, NM_133851, NM_009791, NM_013917, NM_175384, NM_011121, NM_023223, NM_173762, NM_009774, NM_016692, NM_011496, NM_001081363, NM_010891, NM_007628, NM_007659, NM_009860, NM_001040435, NM_027975, NM_007634, NM_153058, NM_026785, NM_001081117, NM_028232, NM_172301, NM_017407

NM_016692, NM_011496, NM_011497, NM_001081363, NM_010891, NM_133851, NM_007628, NM_009791, NM_007659, NM_009860, NM_175384, NM_013917, NM_011121, NM_153058, NM_027975, NM_173762, NM_023223, NM_007634, NM_026785, NM_009774, NM_028232, NM_017407, NM_172301

NM_016692, NM_011496, NM_010891, NM_133851, NM_007628, NM_009791, NM_007659, NM_009860, NM_175384, NM_013917, NM_011121, NM_153058, NM_027975, NM_173762, NM_023223, NM_007634, NM_026785, NM_009774, NM_028232, NM_017407, NM_172301

NM_016692, NM_011496, NM_010891, NM_133851, NM_007628, NM_009791, NM_011623, NM_007659, NM_009860, NM_175384, NM_013917, NM_011121, NM_153058, NM_027975, NM_173762, NM_023223, NM_007634, NM_026785, NM_028232, NM_017407, NM_172301

NM_016692, NM_013917, NM_001081363, NM_001014976, NM_173762, NM_133851, NM_011623, NM_009774, NM_028232

NM_023422, NM_008197, NM_010436, NM_007681, NM_178187, NM_133851, NM_178218, NM_015786, NM_011623, NM_198622

NM_023422, NM_008197, NM_146116, NM_010436, NM_007681, NM_178187, NM_010891, NM_007578, NM_009448, NM_178218, NM_015786, NM_198622

NM_023422, NM_008197, NM_010436, NM_007681, NM_178187, NM_178218, NM_015786, NM_198622

NM_023422, NM_008197, NM_146116, NM_010436, NM_007681, NM_178187, NM_010891, NM_007578, NM_009448, NM_178218, NM_015786, NM_198622

NM_010436, NM_007681, NM_007578, NM_009448, NM_010891, NM_178218, NM_198622, NM_023422, NM_008197, NM_146116, NM_008161, NM_178187, NM_015786

NM_023422, NM_008197, NM_010436, NM_007681, NM_178187, NM_178218, NM_015786, NM_198622

NM_010436, NM_007681, NM_133851, NM_178218, NM_011623, NM_198622, NM_023422, NM_008197, NM_013917, NM_178187, NM_001081102, NM_015786, NM_001098836, NM_009774

NM_010436, NM_007681, NM_007578, NM_009448, NM_010891, NM_178218, NM_198622, NM_023422, NM_008197, NM_146116, NM_008161, NM_178187, NM_015786

NM_013917, NM_001014976, NM_010436, NM_007628, NM_001081117, NM_028232

NM_023422, NM_008197, NM_010436, NM_007681, NM_178187, NM_001081102, NM_178218, NM_015786, NM_001098836, NM_198622

NM_011496, NM_016692, NM_010891, NM_133851

NM_146116, NM_008446, NM_001014976, NM_001040435, NM_173762, NM_009448, NM_133851, NM_009004

NM_013917, NM_001014976, NM_028232

NM_029688, NM_008161, NM_080728, NM_024198, NM_027127

NM_146116, NM_008446, NM_173762, NM_009448, NM_009004

NM_001081363, NM_001040435, NM_133851, NM_009791

NM_010419, NM_008745, NM_011594, NM_007578, NM_009791

NM_001081363, NM_001040435, NM_010104, NM_173762, NM_008745, NM_007578

NM_009876, NM_001079876, NM_028222, NM_021515

NM_013602, NM_008630

NM_001040435, NM_173762, NM_009791

NM_008091, NM_010419, NM_008090

NM_013602, NM_008630, NM_007488

NM_013602, NM_008630

NM_013917, NM_001014976

NM_010419, NM_008745, NM_011594, NM_007578, NM_009791

NM_010104, NM_008175, NM_001015099, NM_010856, NM_007488, NM_001167963, NM_172301, NM_008090

NM_001040435, NM_173762, NM_009791

NM_010496, NM_007778

NM_010104, NM_007578

NM_001081363, NM_173762, NM_133851

NM_007659, NM_001081363, NM_010436, NM_001040435, NM_173762, NM_133851

NM_010419, NM_008745, NM_011594, NM_007578, NM_009791

NM_001081363, NM_001040435, NM_173762, NM_010891

NM_010496, NM_007778

NM_008161, NM_080728, NM_013602, NM_008630

NM_146116, NM_010891, NM_009448

NM_010419, NM_008745, NM_011594, NM_007578, NM_009791

NM_001013377, NM_010436, NM_010104, NM_016681, NM_013602, NM_007659, NM_023048, NM_029523, XM_001480481, NM_008141, NM_054040, NM_178683, NM_008630, NM_024457, NM_016858

NM_007659, NM_001081363, NM_173762, NM_133851

NM_008091, NM_010104, NM_008745, NM_007778, NM_011905

NM_001040435, NM_009697, NM_011261, NM_009791, NM_008090

NM_009876, NM_010419, NM_007578, NM_008090

NM_001081363, NM_001040435, NM_173762

NM_013602, NM_008630

NM_146116, NM_010891, NM_007578, NM_009448

NM_013602, NM_008630

NM_001014976, NM_001040435, NM_173762, NM_133851

NM_007659, NM_010436, NM_173762

NM_010724, NM_023048, NM_054040, NM_001081661, NM_015821, NM_023223, NM_001015099, NM_001167963, NM_026785, NM_001081656, NM_026383

NM_007659, NM_010436, NM_016681

NM_010724, NM_023048, NM_054040, NM_001081661, NM_015821, NM_023223, NM_001015099, NM_001167963, NM_026785, NM_001081656

NM_010104, NM_173762, NM_007778, NM_011261

NM_007578, NM_011261

NM_007659, NM_138606, NM_011496, NM_011497, NM_011121, NM_016681, NM_008745, NM_020572, NM_011261, NM_172301

NM_010104, NM_173762, NM_007778, NM_011261

List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini

117 393 13588 8.8654009265 1.42E-16 1.42E-16

117 283 13588 10.6698076168 8.80E-16 4.40E-16

117 611 13588 6.4626015919 3.95E-15 1.32E-15

117 194 13588 13.1701471495 1.10E-14 2.74E-15

117 328 13588 9.2059620596 3.01E-14 6.03E-15

117 244 13588 10.9473167998 1.10E-13 1.83E-14

117 190 13588 12.8361673414 1.10E-13 1.58E-14

117 197 13588 12.3800598724 2.20E-13 2.75E-14

117 281 13588 8.6792590565 2.45E-10 2.72E-11

117 64 13588 16.3317307692 6.51E-05 6.51E-06

117 101 13588 11.4986883304 1.89E-04 1.72E-05

117 217 13588 6.4223088739 0.0023978404 2.00E-04

117 73 13588 12.7273153027 0.0027891118 2.15E-04

117 75 13588 12.3879202279 0.0033492957 2.40E-04

117 76 13588 12.2249212776 0.0036626898 2.45E-04

117 245 13588 5.6883307169 0.0076681934 4.81E-04

117 338 13588 4.4667981591 0.0304944527 0.0018200524

117 109 13588 8.523798322 0.0389013212 0.0022019162

117 404 13588 4.0245409156 0.0389716046 0.0020899878

117 367 13588 4.1138359068 0.0663827325 0.0034285442

117 88 13588 7.9184149184 0.6010812245 0.0428180531

117 90 13588 7.7424501425 0.6383952395 0.0451838996

117 315 13588 3.6868810202 0.7741143661 0.0626361504

117 27 13588 17.205444761 0.7800808149 0.0611541377

117 211 13588 4.4032891805 0.8875279228 0.0836913452

117 11 13588 31.6736596737 0.9765298433 0.13437949

117 87 13588 6.6745259849 0.9984621279 0.213295091

117 101 13588 5.7493441652 0.9999810824 0.3218642756

117 54 13588 8.6027223805 0.9999819685 0.3138566574

117 102 13588 5.6929780459 0.9999869731 0.3126762473

117 161 13588 4.3280777194 0.9999951742 0.3262445863

117 57 13588 8.1499475184 0.9999968303 0.3267799804

117 2 13588 116.1367521368 0.9999999583 0.4024720456

117 25 13588 13.9364102564 0.9999999948 0.4294909013

117 27 13588 12.9040835708 0.9999999998 0.468381698

117 29 13588 12.0141467728 1 0.5053372425

117 3 13588 77.4245014245 1 0.4978973462

117 132 13588 4.3991193991 1 0.503033354

117 267 13588 3.0447837639 1 0.4995984195

117 33 13588 10.5578865579 1 0.5545871213

117 4 13588 58.0683760684 1 0.5635196667

117 34 13588 10.2473604827 1 0.5572100466

117 214 13588 3.2561706207 1 0.5746680682

117 148 13588 3.9235389235 1 0.5814562261

117 90 13588 5.1616334283 1 0.6085464789

117 5 13588 46.4547008547 1 0.6029375069

117 92 13588 5.0494240059 1 0.6130696133

117 40 13588 8.7102564103 1 0.618965946

117 159 13588 3.6520991238 1 0.6242558522

117 915 13588 1.7769557704 1 0.6237585751

117 96 13588 4.839031339 1 0.6225444147

117 163 13588 3.5624770594 1 0.6306570259

117 167 13588 3.4771482676 1 0.6510437919

117 101 13588 4.5994753321 1 0.6482831382

117 45 13588 7.7424501425 1 0.6486033745

117 7 13588 33.1819291819 1 0.6543364496

117 108 13588 4.3013611903 1 0.6892342524

117 8 13588 29.0341880342 1 0.6903227698

117 111 13588 4.1851081851 1 0.7011129755

117 52 13588 6.7001972387 1 0.7125825325

117 609 13588 1.9070074242 1 0.7245550254

117 57 13588 6.1124606388 1 0.7590040793

117 534 13588 1.9573609911 1 0.758797508

117 537 13588 1.9464260135 1 0.7622174332

117 124 13588 3.7463468431 1 0.7615778598

117 11 13588 21.1157731158 1 0.7574616239

117 640 13588 1.8146367521 1 0.7772586807

117 130 13588 3.5734385273 1 0.7843295942

Supplementary Table 1. LIN9 regulated genes in ES cells

Genes regulated > 1.5 fold after depletion of LIN9

FDR

2.27E-16

1.40E-15

6.28E-15

1.74E-14

4.80E-14

1.78E-13

3.55E-13

3.90E-10

1.04E-04

3.01E-04

0.0038230319

0.0044477193

0.005342505

0.0058433076

0.0122577751

0.0493055711

0.0631668781

0.063283264

0.109325771

1.4528306798

1.60682954

2.3413340317

2.3829557543

3.4198110733

5.8000335977

9.8009030979

15.902149348

15.966373254

16.40030789

17.711949567

18.260916098

23.709242093

26.204513661

29.683392025

33.204167234

33.365157082

34.501037803

34.948642293

40.260125571

41.799531261

42.008821951

44.311571911

45.680382072

48.936849152

49.166824422

50.868861556

52.170902293

53.411217107

54.083482049

54.6742765

56.167874787

58.876373222

59.285129679

59.988966856

61.222864879

65.384240742

66.132476662

67.848230512

69.618100619

71.421347808

75.462298956

75.991457526

76.868193725

77.328364292

77.43784883

79.856855192

81.008048237

Supplementary Table 1. LIN9 regulated genes in ES cells

Table S2

Abstract

File (1)

Linked Research

Recommended publications

S16 Table

Table S1

S7 Table

Table S4