Table S1.
Functional Annotation Clustering of Genes Up-Regulated in Klf4-Null MEFs
| ILLUMINA ID | Gene Symbol | Gene Name (Description) | P-value | Fold-Change |
|---|---|---|---|---|
| Cell Cycle | 8.00E-03 | |||
| ILMN_1217331 | Mcm6 | MINICHROMOSOME MAINTENANCE DEFICIENT 6 | 40.36 | |
| ILMN_2723931 | E2f6 | E2F TRANSCRIPTION FACTOR 6 | 26.8 | |
| ILMN_2724570 | Mapk12 | MITOGEN-ACTIVATED PROTEIN KINASE 12 | 22.19 | |
| ILMN_1218470 | Cdk2 | CYCLIN-DEPENDENT KINASE 2 | 9.32 | |
| ILMN_1234909 | Tipin | TIMELESS INTERACTING PROTEIN | 5.3 | |
| ILMN_1212692 | Mapk13 | SAPK/ERK/KINASE 4 | 4.96 | |
| ILMN_2666690 | Cul7 | CULLIN 7 | 2.23 | |
| ILMN_2681776 | Mapk6 | MITOGEN ACTIVATED PROTEIN KINASE 4 | 2.11 | |
| ILMN_2652909 | Ddit3 | DNA-DAMAGE INDUCIBLE TRANSCRIPT 3 | 2.07 | |
| ILMN_2742152 | Gadd45a | GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE 45 ALPHA | 1.92 | |
| ILMN_1212787 | Pttg1 | PITUITARY TUMOR-TRANSFORMING 1 | 1.8 | |
| ILMN_1216721 | Cdk5 | CYCLIN-DEPENDENT KINASE 5 | 1.78 | |
| ILMN_1227009 | Gas2l1 | GROWTH ARREST-SPECIFIC 2 LIKE 1 | 1.74 | |
| ILMN_2663009 | Rassf5 | RAS ASSOCIATION (RALGDS/AF-6) DOMAIN FAMILY 5 | 1.64 | |
| ILMN_1220454 | Anapc13 | ANAPHASE PROMOTING COMPLEX SUBUNIT 13 | 1.61 | |
| ILMN_1216213 | Incenp | INNER CENTROMERE PROTEIN | 1.56 | |
| ILMN_1256301 | Rcc2 | REGULATOR OF CHROMOSOME CONDENSATION 2 | 1.53 | |
| Extracellular Matrix | 5.80E-06 | |||
| ILMN_2735184 | Col18a1 | PROCOLLAGEN, TYPE XVIII, ALPHA 1 | 51.5 | |
| ILMN_1223997 | Crtap | CARTILAGE ASSOCIATED PROTEIN | 32.74 | |
| ILMN_2753809 | Mmp3 | MATRIX METALLOPEPTIDASE 3 | 31.08 | |
| ILMN_2747959 | Dcn | DECORIN | 21.44 | |
| ILMN_2737685 | Mmp13 | MATRIX METALLOPEPTIDASE 13 | 13.86 | |
| ILMN_1232899 | Smoc2 | SPARC RELATED MODULAR CALCIUM BINDING 2 | 6.91 | |
| ILMN_2727663 | Tgfbi | TRANSFORMING GROWTH FACTOR, BETA INDUCED | 6.75 | |
| ILMN_1258629 | Col3a1 | PROCOLLAGEN, TYPE III, ALPHA 1 | 5.65 | |
| ILMN_2619952 | Mmp10 | MATRIX METALLOPEPTIDASE 10 | 5.32 | |
| ILMN_2668463 | Emilin1 | ELASTIN MICROFIBRIL INTERFACER 1 | 3.99 | |
| ILMN_1230747 | Wnt9a | WINGLESS-TYPE MMTV INTEGRATION SITE 9A | 3.8 | |
| ILMN_1254546 | Col5a2 | PROCOLLAGEN, TYPE V, ALPHA 2 | 3.42 | |
| ILMN_2422848 | Wnt10b | WINGLESS RELATED MMTV INTEGRATION SITE 10B | 2.97 | |
| ILMN_2772556 | Fbn1 | FIBRILLIN 1 | 2.71 | |
| ILMN_2635784 | Gpc | GLYPICAN 1 | 2.37 | |
| ILMN_1238215 | Ctgf | CONNECTIVE TISSUE GROWTH FACTOR | 2.28 | |
| ILMN_2640248 | Lama5 | LAMININ, ALPHA 5 | 2.27 | |
| ILMN_2687880 | Col1a1 | PROCOLLAGEN, TYPE I, ALPHA 1 | 2.06 | |
| ILMN_2769917 | Timp1 | TISSUE INHIBITOR OF METALLOPROTEINASE 1 | 1.99 | |
| ILMN_1225835 | Mfap5 | MICROFIBRILLAR ASSOCIATED PROTEIN 5 | 1.97 | |
| ILMN_1258759 | Col6a2 | PROCOLLAGEN, TYPE VI, ALPHA 2 | 1.77 | |
| ILMN_2497957 | Epb4.1l1 | FIBULIN 1 | 1.76 | |
| ILMN_2678218 | Mmp2 | MATRIX METALLOPEPTIDASE 2 | 1.75 | |
| ILMN_1217071 | Mmp16 | MATRIX METALLOPEPTIDASE 16 | 1.67 | |
| ILMN_2774596 | Lamc | LAMININ, GAMMA 1 | 1.66 | |
| ILMN_1238597 | Omd | OSTEOMODULIN | 1.53 | |
| Ubiquitin | 1.40E-02 | |||
| ILMN_2662401 | Sumo3 | SMT3 SUPPRESSOR OF MIF TWO 3 HOMOLOG 3 (YEAST) | 70.01 | |
| ILMN_2763459 | Tbcel | LEUCINE RICH REPEAT CONTAINING 35 | 3.51 | |
| ILMN_1225261 | UchM | UBIQUITIN CARBOXY-TERMINAL HYDROLASE L1 | 3.02 | |
| ILMN_1229019 | Fbxo44 | F-BOX PROTEIN 44 | 2.12 | |
| ILMN_2749911 | Ube2q2 | UBIQUITIN-CONJUGATING ENZYME E2Q (PUTATIVE) 2 | 1.96 | |
| ILMN_2417991 | Ube2i | UBIQUITIN-CONJUGATING ENZYME E2I | 1.79 | |
| ILMN_1246522 | Uchl3 | UBIQUITIN CARBOXYL-TERMINAL ESTERASE L3 (UBIQUITIN THIOLESTERASE) | 1.63 | |
| ILMN_2495573 | Ubqln1 | DNA SEGMENT, CHR 13, ERATO DOI 372, EXPRESSED | 1.54 | |
| ILMN_2486783 | Ube2d3 | UBIQUITIN-CONJUGATING ENZYME E2D 3 (UBC4/5 HOMOLOG, YEAST) | 1.54 | |
| ILMN_1227863 | Ube2n | UBIQUITIN-CONJUGATING ENZYME E2N | 1.53 | |
| ILMN_2516699 | Ubb | UBIQUITIN B | 1.51 | |
| Proto-oncogenes | 2.70E-03 | |||
| ILMN_2655260 | Ptp4a3 | PROTEIN TYROSINE PHOSPHATASE 4A3 | 4 | |
| ILMN_1233424 | Lbcl | RHO/RAC GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 2 | 2.03 | |
| ILMN_1224526 | Lck | LYMPHOCYTE PROTEIN TYROSINE KINASE | 2 | |
| ILMN_1237241 | Araf | V-RAF MURINE SARCOMA 3611 VIRAL ONCOGENE HOMOLOG | 1.83 | |
| ILMN_1212787 | Pttg1 | PITUITARY TUMOR-TRANSFORMING 1 | 1.8 | |
| ILMN_2481071 | Hras1 | HARVEY RAT SARCOMA VIRUS ONCOGENE 1 | 1.78 | |
| ILMN_1251669 | Evi2a | ECOTROPIC VIRAL INTEGRATION SITE 2A | 1.77 | |
| ILMN_2492264 | Wisp1 | WNT1 INDUCIBLE SIGNALING PATHWAY PROTEIN 1 | 1.76 | |
| ILMN_1221750 | MycM | LUNG CARCINOMA MYC RELATED ONCOGENE 1 | 1.66 | |
| Growth Factors | 2.30E-02 | |||
| ILMN_1238547 | Areg | AMPHIREGULIN | 21.43 | |
| ILMN_1215252 | Bmp4 | BONE MORPHOGENETIC PROTEIN 4 | 14.31 | |
| ILMN_1254114 | Artn | ARTEMIN | 8.65 | |
| ILMN_2763243 | CHEM | CHEMOKINE (C-X-C MOTIF) LIGAND 1 | 8.46 | |
| ILMN_2745480 | Fgf13 | FIBROBLAST GROWTH FACTOR 13 | 6.53 | |
| ILMN_2710698 | Fgf21 | FIBROBLAST GROWTH FACTOR 21 | 5.51 | |
| ILMN_1246073 | Lefty1 | LEFT RIGHT DETERMINATION FACTOR 1 | 4.72 | |
| ILMN_2659994 | Gdnf | GLIAL CELL LINE DERIVED NEUROTROPHIC FACTOR | 3.1 | |
| ILMN_1236725 | Gdf1 | GROWTH DIFFERENTIATION FACTOR 1 | 2.53 | |
| ILMN_2698449 | Hbegf | HEPARIN-BINDING EGF-LIKE GROWTH FACTOR | 2.36 | |
| ILMN_2484527 | Vegfa | VASCULAR ENDOTHELIAL GROWTH FACTOR A | 1.97 | |
| ILMN_2697220 | Figf | C-FOS INDUCED GROWTH FACTOR | 1.74 | |
| ILMN_2736496 | FgflO | FIBROBLAST GROWTH FACTOR 10 | 1.73 | |
| Cell Adhesion | 1.80E-03 | |||
| ILMN_2774764 | Cntnap4 | CONTACTIN ASSOCIATED PROTEIN 4 | 7.88 | |
| ILMN_2627041 | Cx3cl1 | CHEMOKINE (C-X3-C MOTIF) LIGAND 1 | 2.5 | |
| ILMN_2670172 | Itga5 | INTEGRIN ALPHA 5 (FIBRONECTIN RECEPTOR ALPHA) | 2.32 | |
| ILMN_2640248 | Lama5 | LAMININ, ALPHA 5 | 2.27 | |
| ILMN_1223697 | Cd44 | CD44 ANTIGEN | 2.1 | |
| ILMN_1243254 | Adam12 | A DISINTEGRIN AND METALLOPEPTIDASE DOMAIN 12 (MELTRIN ALPHA) | 1.92 | |
| ILMN_2707976 | Cdh26 | CADHERIN-LIKE26 | 1.88 | |
| ILMN_2725411 | Cd9 | CD9 ANTIGEN | 1.84 | |
| ILMN_1257880 | Itga7 | INTEGRIN ALPHA 7 | 1.77 | |
| ILMN_2492264 | Wisp1 | WNT1 INDUCIBLE SIGNALING PATHWAY PROTEIN 1 | 1.76 | |
| ILMN_2663613 | Itgb5 | INTEGRIN BETA 5 | 1.74 | |
| ILMN_2659503 | Cdh13 | CADHERIN 13 | 1.69 | |
| ILMN_1241893 | Wisp2 | WNT1 INDUCIBLE SIGNALING PATHWAY PROTEIN 2 | 1.69 | |
| ILMN_1232768 | Vcam1 | VASCULAR CELL ADHESION MOLECULE 1 | 1.56 | |
| ILMN_1237629 | Cntn2 | CONTACTIN 2 | 1.51 | |
| Collagen | 2.10E-02 | |||
| ILMN_2735184 | Col18a1 | PROCOLLAGEN, TYPE XVIII, ALPHA 1 | 19.16 | |
| ILMN_1258629 | Col3a1 | PROCOLLAGEN, TYPE III, ALPHA 1 | 5.65 | |
| ILMN_1254546 | Col5a2 | PROCOLLAGEN, TYPE V, ALPHA 2 | 3.04 | |
| ILMN_2687880 | Col1a1 | PROCOLLAGEN, TYPE I, ALPHA 1 | 2.06 | |
| ILMN_2707616 | Col22a1 | COLLAGEN, TYPE XXII, ALPHA 1 | 1.87 | |
| ILMN_1258759 | Col6a2 | PROCOLLAGEN, TYPE VI, ALPHA 2 | 1.77 | |
| ILMN_1225073 | Cthrc | COLLAGEN TRIPLE HELIX REPEAT CONTAINING 1 | 1.53 | |
| Inflammatory Response | 1.60E-02 | |||
| ILMN_1230789 | C3 | COMPLEMENT COMPONENT 3 | 8.8 | |
| ILMN_2763243 | CHEM | CHEMOKINE (C-X-C MOTIF) LIGAND 1 | 8.46 | |
| ILMN_2742075 | Cd14 | CD14 ANTIGEN | 2.68 | |
| ILMN_1254383 | Atrn | ATTRACTIN | 1.99 | |
| ILMN_1259252 | Anxa1 | ANNEXINA1 | 1.99 | |
| ILMN_1255385 | Chst1 | CARBOHYDRATE (KERATAN SULFATE GAL-6) SULFOTRANSFERASE 1 | 1.82 | |
| Chemotaxis | 1.50E-02 | |||
| ILMN_1231814 | Ccl5 | CHEMOKINE (C-C MOTIF) LIGAND 5 | 13.25 | |
| ILMN_2772998 | Enpp2 | ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE 2 | 12.7 | |
| ILMN_2658910 | Cxcl12 | CHEMOKINE (C-X-C MOTIF) LIGAND 12 | 6.78 | |
| ILMN_1245710 | Ccl2 | CHEMOKINE (C-C MOTIF) LIGAND 2 | 5.47 | |
| ILMN_1253797 | Slit2 | SLIT HOMOLOG 2 (DROSOPHILA) | 3.1 | |
| ILMN_1214419 | CHEMO | CHEMOKINE (C-X-C MOTIF) LIGAND 10 | 2.94 | |
| ILMN_1235571 | Cyr61 | CYSTEINE RICH PROTEIN 61 | 2.9 | |
| ILMN_1216285 | Creb3 | CAMP RESPONSIVE ELEMENT BINDING PROTEIN 3 | 1.55 | |
| Development | 3.10E-02 | |||
| ILMN_1234990 | Gap43 | GROWTH ASSOCIATED PROTEIN 43 | 37.4 | |
| ILMN_1226016 | Scx | SCLERAXIS | 29.89 | |
| ILMN_1215252 | Bmp4 | BONE MORPHOGENETIC PROTEIN 4 | 14.3 | |
| ILMN_2769657 | Picalm | PHOSPHATIDYLINOSITOL BINDING CLATHRIN ASSEMBLY PROTEIN | 4.98 | |
| ILMN_1246073 | Lefty1 | LEFT RIGHT DETERMINATION FACTOR 1 | 4.71 | |
| ILMN_2684289 | Sema3a | SEMA DOMAIN, IMMUNOGLOBULIN DOMAIN (IG), SHORT BASIC DOMAIN, SECRETED, | 3.89 | |
| ILMN_1230747 | Wnt9a | WINGLESS-TYPE MMTV INTEGRATION SITE 9A | 3.8 | |
| ILMN_2422848 | Wnt10b | WINGLESS RELATED MMTV INTEGRATION SITE 10B | 2.97 | |
| ILMN_2675833 | Dlx3 | DISTAL-LESS HOMEOBOX 3 | 2.96 | |
| ILMN_1245731 | Hhex | HEMATOPOIETICALLY EXPRESSED HOMEOBOX | 2.82 | |
| ILMN_1238558 | Arid3b | AT RICH INTERACTIVE DOMAIN 3B (BRIGHT LIKE) | 2.35 | |
| ILMN_1225378 | Htatip2 | HIV-1 TAT INTERACTIVE PROTEIN 2, HOMOLOG (HUMAN) | 1.99 | |
| ILMN_1252870 | Rorb | RAR-RELATED ORPHAN RECEPTOR BETA | 1.89 | |
| ILMN_2722938 | Myd116 | MYELOID DIFFERENTIATION PRIMARY RESPONSE GENE 116 | 1.84 | |
| ILMN_2697220 | Figf | C-FOS INDUCED GROWTH FACTOR | 1.74 | |
| ILMN_1223414 | Ptp4a1 | PROTEIN TYROSINE PHOSPHATASE 4A1 | 1.72 | |
| ILMN_1215746 | Cchcr | COILED-COIL ALPHA-HELICAL ROD PROTEIN 1 | 1.65 | |
| ILMN_2734034 | Prrx2 | PAIRED RELATED HOMEOBOX 2 | 1.55 | |
| ILMN_2630811 | Rere | ARGININE GLUTAMIC ACID DIPEPTIDE (RE) REPEATS | 1.54 | |
| ILMN_2706755 | Foxd1 | FORKHEAD BOX D1 | 1.54 | |
| ILMN_1238875 | Strbp | SPERMATID PERINUCLEAR RNA BINDING PROTEIN | 1.54 | |
| ILMN_1253420 | Psme4 | PROTEASOME (PROSOME, MACROPAIN) ACTIVATOR SUBUNIT 4 | 1.5 | |
| Other Genes | ||||
| ILMN_1218967 | Kif2c | KINESIN FAMILY MEMBER 2C | 37.42 | |
| ILMN_2611181 | Ccdc3 | COILED-COIL DOMAIN CONTAINING 3 | 36.32 | |
| ILMN_1217009 | Rab15 | RAB15, MEMBER RAS ONCOGENE FAMILY | 33.76 | |
| ILMN_2621448 | Adh7 | ALCOHOL DEHYDROGENASE 7 (CLASS IV), MU OR SIGMA POLYPEPTIDE | 22.19 | |
| ILMN_1245531 | Neto2 | NEUROPILIN (NRP) AND TOLLOID (TLL)-LIKE 2 | 21.94 | |
| ILMN_1225602 | S100a1 | S100 CALCIUM BINDING PROTEIN A1 | 20.27 | |
| ILMN_2703267 | Nes | NESTIN | 18.5 | |
| ILMN_1245451 | Rab6b | RAB6B, MEMBER RAS ONCOGENE FAMILY | 14.71 | |
| ILMN_2713285 | Fhl1 | FOUR AND A HALF LIM DOMAINS 1 | 14.19 | |
| ILMN_2606660 | Card 10 | CASPASE RECRUITMENT DOMAIN FAMILY, MEMBER 10 | 10.23 | |
| ILMN_2646891 | Centd1 | CENTAURIN, DELTA 1 | 9.05 | |
| ILMN_2686327 | Gas6 | GROWTH ARREST SPECIFIC 6 | 8.94 | |
| ILMN_2689998 | Fjx1 | FOUR JOINTED BOX 1 (DROSOPHILA) | 8.81 | |
| ILMN_1230080 | S100a7a | S100 CALCIUM BINDING PROTEIN A15 | 6.95 | |
| ILMN_1247646 | H1fx | H1 HISTONE FAMILY, MEMBER X | 6.91 | |
| ILMN_1217159 | Lmo7 | LIM DOMAIN ONLY 7 | 5.51 | |
| ILMN_1214327 | S100a13 | S100 CALCIUM BINDING PROTEIN A13 | 5.19 | |
| ILMN_1242829 | Prdx2 | PEROXIREDOXIN 2 | 5.10 | |
| ILMN_2868133 | Gata6 | GATA BINDING PROTEIN 6 | 4.75 | |
| ILMN_2614590 | Tmem45a | TRANSMEMBRANE PROTEIN 45A | 4.71 | |
| ILMN_1224014 | Tmem100 | TRANSMEMBRANE PROTEIN 100 | 4.42 | |
| ILMN_1230586 | Traf1 | TNF RECEPTOR-ASSOCIATED FACTOR 1 | 3.73 | |
| ILMN_1215807 | Glipr1 | GLI PATHOGENESIS-RELATED 1 (GLIOMA) | 3.44 | |
| ILMN_2633670 | Tmem62 | TRANSMEMBRANE PROTEIN 62 | 3.03 | |
| ILMN_2773901 | Glipr2 | GLI PATHOGENESIS-RELATED 2 | 3.02 | |
| ILMN_1227993 | Vav3 | VAV 3 ONCOGENE | 2.67 | |
| ILMN_2714361 | Cd34 | CD34 ANTIGEN | 2.32 | |
| ILMN_2687880 | Col1a1 | PROCOLLAGEN, TYPE I, ALPHA 1 | 2.02 | |
| ILMN_1214227 | Krt1-10 | KERATIN COMPLEX 1, ACIDIC, GENE 1-10 | 1.84 | |
The criteria for Functional Annotation Clustering of Gene analysis was set at P < 0.05 and fold-change less than or equal to 1.5. Shown are functional clusters of genes that were up-regulated in Klf4-null MEFs.