Genotyping, IgA measurement, Western blotting, Histopathological analysis, RNA expression analysis, Immunofluorescence and Immunohistochemistry, RT-qPCR, SNP analysis, FACS and Microscopy
Human, Mice
TNF
Tumor necrosis factor
IBD, UC, CD
7124
22848538, 27895399, 12671897
Fish, qPCR, Histopathology, ELISA, Cytokine staining, RT-PCR and Western blotting
mice and Human
RIPK2
Receptor interacting serine/threonine kinase 2
IBD, CD
8767
26320862
Immunoblotting, qPCR and Flow cytometry
Human
TLR2
Toll like receptor 4
CD, UC, IBD
7097
28388655, 22434667, 19950179
Genotyping, SNP analysis, qPCR and FACS
Mice and Bacteria
TLR4
Toll like receptor 3
UC, CD, IBD
7099
29913461, 19664207, 17538633
qPCR and Western blotting, RFLP
Human
IL23R
Interleukin 23 receptor
IBD, UC, CD
149233
17447842, 17786191, 17030949
SNP analysis, FRET, qPCR, ELISA and FACS
Human, Mice
IRGM
Immunity related GTPase M
CD, UC, IBD
345611
20106866
Microarray expression analysis, qPCR, SNP analysis
Human
TLR3
Toll like receptor 3
IBD, UC
7098
28099447
1D SDS-PAGE, 2D Gel analysis and Gene expression
GAPDH
Glyceraldehyde-3-phosphate dehydrogenase
IBD, CD
2597
27812135, 19907652
(GWAS) RT-qPCR, Immunoblotting, ELISA, BRET analyses, Immunoprecipitation experiments, Yeast two-hybrid screening, SNP genotyping, siRNAs and NF-kappaB reporter assays, Western blotting with anti-MYC and anti-GFP antibodies
PTPN2
Protein tyrosine phosphatase non-receptor type 2
IBD, CD, UC
5771
22457781
(GWAS) PCR, DNA extraction, FRET and SNP genotyping, In silico analysis of transcription factor binding sites, Haplotype analysis
Human
MUC2
Mucin 2, oligomeric mucus/gel-forming
IBD, UC, CD
4583
27490946
Immunochip, High throughput sequencing
PIGR
Polymeric immunoglobulin receptor
IBD, CD, UC
5284
22491177
RT-qPCR, Tissue histology and Immunofluorescence microscopy
Down
BAHD1
Bromo adjacent homology domain containing 1
UC
22893
26183847
Immunohistochemistry, RT-qPCR, Western blot, ELISA, DSS induced colitic mice
Human, C57BL/6 Mice
Down
FFAR2
Free fatty acid receptor 2
IBD
2867
27667443
Immunohistochemistry, RT-qPCR, Western blotting
Down
FFAR3
Free fatty acid receptor 3
IBD
2865
27667443
Immunohistochemistry, RT-qPCR, Western blotting
Down
NCF2
Neutrophil cytosolic factor 2
UC
4688
21900546
Western blot, Cell culture and Immunoprecipitation, RT-PCR, Cell adhesion assay, NCF2 genotyping, SNP analysis and Genotyping, Subphenotype analysis, Apoptosis analysis
Up
RAC2
Rac family small GTPase 2
IBD, UC
5880
21900546
RT-PCR, Apoptosis analysis, SNP analysis and genotyping, Cell adhesion assay, Subphenotype analysis, Constructs, Western blot, Cell culture and Immunoprecipitation
Up
NCF4
Neutrophil cytosolic factor 4
CD
4689
21900546, 26289090
SNP genotyping and analysis, Subphenotype analysis, RT-PCR
Up
SEL1L
SEL1L adaptor subunit of ERAD E3 ubiquitin ligase
UC
6400
26551274
Western blot, Knockdown, RT-qPCR, Immunohistochemistry
Down
GLI1
GLI family zinc finger 1
UC
2735
19071955
RT-qPCR, SNP genotyping, Gene expression by microarray, NanoDrop ND-1000 spectrophotometer, Induction of DSS-induced colitis and Histological analysis, Immunohistochemistry, GLI1 protein mutagenesis, Luciferase assay and Immunofluorescence, Cytokine expre
Gli1+/lacZ Mice
Down
PTCH1
Patched 1
UC
5727
16733713
DNA extraction, SNP genotyping
Human
Down
IHH
Indian hedgehog signaling molecule
CD
3549
19071955, 20206176, 18479261
ELISA, DAVID, RT-qPCR
C57BL/6 mice
Up
AVIL
Advillin
IBD
10677
12034507
PCR, Mapping of AVIL by Fish, SNP analysis, Lightcycler analysis of AVIL mRNA expression, RT-PCR
qPCR, In vivo injection of heat-killed C.albicans in PBS, Ex vivo splenic stimulations and intracellular phosphoprotein staining, FACS, Bead based-ELISA, Western blotting, Immunoprecipitation
DSS-induced colitis model, Immunoblot, Immunofluorescence staining, qPCR, Ex vivo T-cell Stimulation, PBMC culture, FACS canto II Flow cytometer, Fcap array
Human, Mice
TNFAIP3
TNF alpha induced protein 3
UC, CD
7128
25956706
Multivariate analysis of biomarker expression in colonic mucosa, Taqman gold RT-PCR, mRNA transcripts analyzed by RT-qPCR
Human
CD14
CD14 molecule
CD, UC
929
15764151, 15655821
RFLP-PCR, Genotyping
Human cohort
NLRP12
NLR family pyrin domain containing 12
IBD, CD
91662
22094258, 31169706, 20403135
In situ intestinal proliferation assay, In vitro signaling assays, Multiplex ELISA, qPCR, Induction of DSS induced colitis, Histopathological analysis, Bone marrow chimeras, Isolation of lamina propria cells, NF-KappaB activity assay
Antibodies and Western blotting, NOD signaling defects and cell death susceptibility, CRISPR/SPCAS9 knockout of XIAP and stable cell line generation, qPCR, TNF and LPS cytotoxicity assays, Propidium iodide influx assays, Acquisition of patient PBMCs and F
XIAP/ mice
APC
APC regulator of WNT signaling pathway
UC, IBD
324
9744312, 17192888
PCR, PAGE, Ileorectal anastomosis (IRA), in vitro synthe-sized protein (IVSP)
DLG5
Discs large MAGUK scaffold protein 5
CD, IBD, UC
9231
16494592, 15107852
Genotyping for DLG5 variants, PCR, FRET probes, Measurement of gastro-duodenal and intestinal permeability, Genotyping for Card15 variants, SNPs genotyping analysis, Microsatellite typing
Human
DMBT1
Deleted in malignant brain tumors 1
CD, IBD
1755
17983803, 24223725
siRNA transfection, qPCR, Western blot, Electrophoretic mobility shift, Luciferase assays, RT-qPCR, Immunohistochemistry, mRNA In situ hybridization, Haplotype association
Human, Mice
DMBT SNP�s; Up
TNFRSF17
TNF receptor superfamily member 17
IBD
608
16318629
SNP genotyping, Tailed primer PCR, Microsatellite markers analysis
Human
KLF6
Kruppel like factor 6
IBD
1316
26838049
Western blot, RT-PCR, Immunofluorescent confocal staining
Mice
Up
FUT3
Fucosyl transferase 3 (Lewis Blood Group)
UC
2525
26766790
SNP genotyping, Immunohistochemistry
Human
FUT3 polymorphisms overrepresented in UC patients vs controls
Genotype analysis By multiplex SNAP assay of Abi, Multiplex PCR, SNP tested in replication of FUT loci by taqman minor groove binder chemistry, Taqman SNP genotyping assays
Human cohort
IBD2
Inflammatory bowel disease 2
IBD, UC
3378
12439891
Genotyping, PCR, Electrophoretic mobility shift assay (EMSA), Criterion blotter, Chemiluminescent nucleic acid detection module (Pierce Biotechnology, Rockford, Il, Usa)
Human
IRF5
Interferon regulatory factor 5
IBD, UC, CD
3663
20127100, 22257839, 3809990, 25564941
Bisulfite pyrosequencing, CpG density calculation
Human
NLRX1
NLR family member X1
IBD
79671
29535731
Experimental model of colitis, Histopathology, Olympus microscope, qPCR, RNA sequencing
Direct genome sequencing, PCR-RFLP, Association study of HLA_DRB1
Human cohort
MST1
Macrophage stimulating 1
IBD, UC, CD
4485
19657358, 19079170, 22087277, 18438406, 21931648
(GWAS) Genotyping by Taqman assays, Fast qPCR, SNP analysis, SNP Selection from hapmap database, Mass spectrometry analysis, Allelic tests, RT-PCR, SNP genotyping with infinium I assay (Illumina), Plink, MALDI-TOF mass array platform
Human cohort
CUL2
Cullin 2
IBD, CD
8453
23639549, 30228239
(GWAS) SNP Test, RT-PCR, Gtex SNP(rs12248333), IBD-associated SNP (rs34779708), EQTL analysis, Haplotype analyses, Selection analyses, Credible set analysis, E. Histolytica culture, Cre-luciferase reporter assays, Crem expression In Q223R mice, Caspase-3
SV129/Bl6.CREM_/_ Mice
FOXP3
Forkhead box P3
IBD, UC
50943
27178149, 28337881
(GWAS) qPCR, mRNA expression, Measurement of serum retinol levels by HPLC, Immunohistochemistry, Histopathology
Human
DUOX2
Dual oxidase 2
IBD, CD, UC
50506
26301257, 25003194, 17454855
Epifluorescence light microscope (Leica microsystems, Buffalo Grove, Il), Protein isolation, Western blotting, Ros assays, Flow cytometry, Immunofluorescence, Virulence assay, Cytoscape.V3.0.2, Immunohistochemistry, Olympus Bx51 light microscope, RT-PCR
Huamn
IL2
Interleukin 2
UC, IBD, CD
3558
21648020, 19201773, 19471255, 8100205, 12591057
SNP analysis, Taqman technology for genotyping, Mass spectrometric analysis, ELISA, ADCC assay, Imminofluorescence staining, Flow cytometry
Human
MYC
MYC proto-oncogene, BHLH transcription factor
IBD, CD
4609
1612482
RNA preparation, Slot blot hybridization, Northern hybridization, in vitro translation, Immunohistochemical studies, expression of C-Myc proto-oncogene
Human
IL22
Interleukin 22
UC, CD
50616
16537974, 26994530
RT-PCR, qPCR, Signal-transduction experiments, Gel electrophoresis, Immunoblotting, ELISA, Wounding assay, Cell proliferation assay, Apoptosis assays, DSS induced colitis model
Mice, Human
Up
HDAC6
Histone deacetylase 6
IBD
10013
27827303
Light microscope, DSS induced colitis, Histology, Mucin staining, Esterase staining, Gut cell isolation, Flow cytometry, RT-PCR analysis, Isolation of human polymorphonuclear leukocytes, HPLC, MS
Female C57BL/6 mice
DEFB1
Defensin beta 1
CD
1672
17921115, 22522766
RT-PCR, Fluorescent microscope, qPCR, DEFB1 SNP genotyping
Human cohort
BIRC3
Baculoviral IAP repeat containing 3
UC
330
23388545
RNA extraction, Microarray analysis, Gene filtering and sample classification were performed using Dchip software, qPCR, Immunohistochemistry
Human
RNF186
Ring finger protein 186
UC
54546
24068945, 27503255
(GWAS) DNA preparation and pooling, PCR, Target selection and design, Sequencing and variant discovery, Genotyping, Validation and follow-up genotyping using sequenom mass array Iplex200, Network analyses, Exome sequencing, MALDI-TOF, Immunofluorescence,
Human cohort, Mice
CRP
C-Reactive protein
pIBD, CD, UC
1401
16497618, 25636121, 18566104
Genotyping, PCR-RFLP, SNP selection, DNA extraction from venous whole blood by salting out technique, Response to anti�TNF_ monoclonal antibody
Human cohort
IL2RA
Interleukin 2 receptor subunit alpha
UC, IBD
3559
23972291, 19471255
Genotyping using primer extension chemistry and Mass spectrometric analysis(Iplex assay, Sequenom, San Diego, Ca), Multiplex PCR, MALDI-TOF Mass spectrometry, Genotyping by Taqman assays from applied biosystems
CD40
CD40 molecule
IBD, CD, UC
958
15591506, 10566730, 16149136
Elucidation of the sequence of rat CD40 mRNA, Immunohistochemistry, Fluorescein (FITC), Immunofluorescence microscopy, Transfection of antisense oligonucleotides(ODNS) in vitro, Western blot analysis, RT-PCR analysis, Colitis induction, Flow cytometric an
Rat
MEFV
MEFV innate Immuity regulator, Pyrin
CD
4210
22810105, 15667491
(GWAS) Genotyping for The MEFV variants, PCR
Human
AIM2
Absent in melanoma 2
UC
9447
26313692, 26655906
Histopathological examination, Affymetrix microarrays, RT-qPCR, RNA isolation, RNA quantity and quality assessed using nanodrop Nd-1000 spectrophotometer, Microarray gene expression data analysed using limma, Immunohistochemistry, Western blot analysis, P
Human Cohort, Mice
Down
BIRC2
Baculoviral IAP repeat containing 2
UC
329
30005591, 28422189
(GWAS) Geo data collection and preprocessing, Network clustering by DPCLUSO, DEGs
UP
CCL5
C-C motif chemokine ligand 5
IBD, UC
6352
19639558, 11872088
qPCR, Immunocytochemistry, Proteomics, Histopathology, Microarray analysis, (LC/MS/MS), Microbial analysis by denaturing gradient gel electrophoresis (DGGE), Sequencing of DGGE bands
Mice IL10-KO and wildtype (WT)
Down
ATG7
Autophagy related 7
UC
10533
30669622, 19139628
(GWAS) Lysozyme staining, The role of the autophagy pathway in paneth cell abnormalities
Mice
AKT1
AKT Serine/Threonine kinase 1
IBD
207
28659381
Induction of colitis, Haematoxylin and Eosin staining, Immunohistochemistry, HCT-8 and Hela cells were used for transfection, Western blot, qPCR, Rt_ Profiler� PCR array data analysis web-based tool (Qiagen, Sa Biosciences, Usa), Immunoprecipitation, ELIS
Proline-serine-threonine phosphatase interacting protein 1
IBD
9051
19731031
EDTA, DHPLC, PCR, PSTPIP1 Microsatellite identification and typing, Genomatix suite used for promoter sequences
Human
Gene Symbol
Full name
Phenotypes
Entrez_id
PMID
Experimental evidences
Sample
Up OR Down
PGLYRP1
Peptidoglycan recognition protein 1
IBD
8993
20709292, 23840689
Western blotting, PGRP-Deficient mice have higher susceptibility to DSS induced colitis, Flow cytometry, RT-qPCR, Cell isolation, Culture, Cytokine production, Amino acid sequence homology in mammalian PGLYRPS in the regions of non-synonymous polymorphism
Mice BALB/c
CD80
CD80 molecule
IBD, UC, CD
941
25595911, 14530338
Flow cytometry, Histopathology, Immunohistochemistry, RT-qPCR, Immunoassay, Induction of colitis and treatments, Cytokine ELISA
C57Bl6/J Mice, BALB/c mice
ICOSLG
Inducible T cell costimulator ligand
IBD, CD
23308
24837102, 20176734, 21072187
(GWAS) FACS, ELISA, Transfection of small interfering RNAs (siRNAs), Western blot, qPCR, Genotyping and association tests
Human, Mice
ITLN1
Intelectin 1
CD
55600
18587394
(GWAS) Haplotype patterns, Hapmap SNPs, EQTL analysis, SNP analysis
IL9
Interleukin 9
UC, IBD
3578
28652656, 25838986, 26377844
Flow cytometry based method utilizing magnetic microspheres, High-sensitive C-reactive protein (HSCRP), Fluorescence based assay, qPCR, Western blot analysis, RT-PCR, Immunofluorescence microscopy, TNBS colitis model, Immunofluorescence staining, ELISA
BALB/c and IL-9 deficient mice
up-regulation
IFNG
Interferon gamma
UC
3458
20848535, 25171510
(GWAS) IFN-assay By ELISA, Pyrosequencing, Hot-start PCR, Isolation of T cells
Human
IL13RA2
Interleukin 13 receptor subunit alpha 2
IBD
3598
22741617, 28612843, 20014020, 30663072
PCR-RFLP, SNP analysis, Immunohistochemistry
Balb/c mice, Human
ZNF365
Zinc finger protein 365
CD
22891
21257989, 20222910, 25489960
RNase minikit (Qiagen, Valencia, Ca), SNP selection and genotype, RT-PCR, Illumina total prep RNA amplification kit (protocol from Ambion, Austin, Tx), Nanodrop spectrophotometer, qPCR
Bradford assay, Immunostaining, Immunohistochemistry, Immunofluorescence and Goblet cell count used as a secondary antibody, Western blot, FITC, RT-qPCR, Chromatin immunoprecipitation (Chip) assay
Human
HNRNPA1
Heterogeneous nuclear ribonucleoprotein A1
CD
3178
19349988
Immunoblot analysis, Chip, RT-PCR, DNA affinity binding assay, Retroviral and Lentiviral packaging and macrophage transduction, Immuno-precipitation, Nanoflol Liquid chromatography�tandem MS analysis, ELISA
Mice
KCNN4
Potassium calcium-activated channel subfamily N member 4
CD
3783
20407432
RT-PCR, qPCR, Immunohistochemistry, MALDI-TOF mass spectrometer, SNP identification and genotyping, Sequenom mass-array assay
Mice, Human
SIGIRR
Single Ig and TIR domain containing
UC
59307
21077278, 20130217
Immunoprecipitation (Chip) assays, Human IL-8 enzyme immune assay (EIA), FITC, qPCR, Immunohistochemistry assays, Flow cytometry, RNA interference, Transient transfection and NF-KappaB, Luciferase assay, Chromatin immunoprecipitation (Chip) assay, Gel shi
Mice
Down
ORMDL3
ORMDL Sphingolipid biosynthesis regulator 3
CD
94103
21072187, 27932194, 28333149, 20228799
(GWAS) SNP genotyping assay(Taqman�), qPCR, SNP analysis, DSS-induced colitis in mice
(GWAS) Microarray analysis of RNA expression, RT-PCR, Data analysis, NCBI gene expression omnibus (Geo), qPCR, Library preparation and Next-generation sequencing with the SeqCap Epi CpGiant enrichment kit
Human
Up
CCL21
C-C motif chemokine ligand 21
UC, CD
6366
24841666, 16118351, 26520877
Immunohistochemistry, DSS induced colitis, RT-PCR, Western blotting, Dapi, Immunohistochemistry staining in the intestinal mucosa of mice
Balb/c mice
Up
ATG16L2
Autophagy related 16 Like 2
CD
89849
27611316, 23850713
(GWAS) Genotyped using taqman SNP genotyping assay, Relationship between genotypes and phenotypes, qPCR, Bioinformatics analysis, mRNA expression of ATG16L2, Imputation
Immunohistochemical staining, Quantification of cytokines using a bead cytometric bead array mouse inflammation kit, Assay for cathepsin activities, DSS induced colitis model, Bone marrow transplantation, Stimulation of mice with NOD ligands, Flow cytomet
Cloning, Expression, Protein purification, Crystallization, Data collection, Structure determination, Protein lipid overlay assay, in vitro caspase cleavage assay, SDS-PAGE, Nanodrop Nd-1000, RT-PCR, Gene expression analysis and Data preprocessing, Genoty
Human
EGFR
Epidermal growth factor receptor
UC
1956
24391216, 29904166
DSS-induced colitis, Western blot analysis, Multi-color flow cytometry, Myeloperoxidase (MPO) assay, Immunophenotyping, Colonic macrophage isolation, Isolation of spleen lymphocytes, qPCR, ELISA, Luciferase activity, SDS-PAGE, Immunohistochemistry, FITC,
Egfrfl/flLysM-Cre mice and UC Human
MAPK3
Mitogen-activated protein kinase 3
IBD, CD
5595
26636514
Bioinformatic analysis, Affymetrix microarray data, Identification of differentially expressed genes, Gene ontology and pathway enrichment analysis of DEGs using Kegg, Go and David, PPI Network and Module analysis, RT-qPCR analysis
Human, Rats
MAP3K8
Mitogen-activated protein kinase 8
IBD, UC
1326
26215868
Transfection of small interfering RNAs (SiRNAs) and Plasmids, Protein expression analysis, mRNA expression analysis, qPCR, RT-PCR, Genotyping, Primary human myeloid cells from IBD, Flow cytometry
Human
RNF31
Ring finger protein 31
IBD, UC
55072
31132297
Human cohort and microarray analysis, Evaluation of mouse colitis, Immunohistochemistry and Immunofluorescent hybridisation, Reagents and antibodies
Male BALB/c mice
Up
IL31RA
Interleukin 31 receptor A
IBD, UC
133396
17449633
RT-PCR, qPCR, SYBR green PCR kit, Signal transduction experiments, Gel electrophoresis, Immunoblotting, Immunofluorescence staining, ELISA, Cell proliferation and cell restitution assays, Murine cytomegalovirus infection in vivo
C57BL/6 wild type Mice
Up
IL21
Interleukin 21
UC
59067
21648020
SNP genotyping, qPCR
Human
IL15
Interleukin 15
UC, CD
3600
10725717, 26964669
FITC or Pe-conjugated anti-CD3, Flow cytometric analysis, Immunohistochemistry, IL-15 production by LPMC, T cell activation by IL-15, Measurement of cytokines, ELISA, In situ expression of IL-15 In intestinal tissue
Human
ATG4D
Autophagy related 4D cysteine peptidase
CD
84971
22261526
(GWAS) Genotyping, RFLP
Human
LACC1
Laccase domain containing 1
CD
144811
27959965, 27098602
Western blot, Transfection, Bradford colorimetric assay, SDS PAGE, Immunofluorescence staining, Antibodies used for immunofluorescence and western blot, Laccase assay, qPCR, FACS flow cytometry, In silico analyses, SNP genotype
Human
Up
FASLG
Fas ligand
CD, IBD, UC
356
22860894, 26374830, 9771405
Genotyping, Immunohistochemistry, Assessment of immunohistochemical staining, RT-PCR, In situ hybridization, Flow cytometry
Human, Mouse
IL7
Interleukin 7
IBD, CD
3574
23057802, 18097039
Induction of colitis and antibody treatments, Pathology and Immunohistochemistry, Serum cytokines and anti-Hb antibodies, Quantitative RT-PCR analyses, ELISA, Flow cytometry
(GWAS) Genotyping using illumina omniexpress, Omni express exome and Omni1-quad arrays, 7900Ht fast qPCR system, UCSC genome bioinformatics and Genecards were utilized, SNP was performed using the encode, Genotype tissue expression (Gtex)29
Human
Up
THY1
Thy-1 cell surface antigen
UC
7070
22826509, 22202458
(GWAS) Qiaamp tissue DNA preparation kit (Qiagen), Three-layer genome wide scans for differential gene expression, Discordant for UC, Expression profiling (mRNA, Layer I), Human methylation27 beadchips (Iscan System, Illumina), Validation of differential
Human
Up
IFNA1
Interferon alpha 1
CD
3439
7861027
Dot blot analysis
Human
Up
CD86
CD86 molecule
IBD, CD, UC
942
18069758, 9438323
PCR, Immunocytometry, Flow cytometric analysis
Human
Up
CSF2
Colony stimulating factor 2
UC, CD
1437
29434451, 19230854
ELISA
Human
Up
TP53
Tumor protein P53
UC, CD
7157
20110711, 17676397
SNP genotyping, Immunohistochemistry staining
Human
Up
CEACAM6
CEA cell adhesion molecule 6
CD
4680
19737864
Histological analyses, Confocal microscopy
Mice
Up
CXCL8
C-X-C motif chemokine ligand 8
CD
3576
15214047
Immunohistochemical staining, ELISA
Human
Down
Gene Symbol
Full name
Phenotypes
Entrez_id
PMID
Experimental evidences
Sample
Up OR Down
ATG5
Autophagy related 5
CD
9474
27096233
SNP genotyping
Human
Down
NFKB1
Nuclear factor Kappa B subunit 1
CD
4790
18092345, 17049230, 24945726
Chemiluminescence, Western blot, SNP genotyping, RT-qPCR, Immunohistochemical staining
Human
Up
LRP6
LDL receptor related protein 6
CD
4040
22393312
SNP genotyping, qPCR, Immunohistochemistry
Human
Down
STAT1
Signal transducer and activator of transcription 1
UC
6772
27220814, 23128233, 12171960
Flow cytometry FACS aria cytometer, LPMCs were cultured in 200 ml complete medium in 96-well plates, qPCR, Multiplex ELISA, Staining of cells for phenotyping and counting, Plasmacytoid dendritic cell isolation kit, PBMCs were isolated by density-gradient
Human
Up
IL10
Interleukin 10
CD
3586
16043989, 29023267, 24128120, 24216686
Abi Prism 3100 automatic sequencer (applied biosystems, Foster City, Calif), Genemapper V3.0 (applied biosystems), SNP genotyping, qPCR, FACS canto II Flow cytometer, Analyzed using flowjo, Ingenuity pathway analysis, RNA in situ hybridization, Immunochem
Mice(Il10-/- and Il10rb-/- mice)
DEFA6
Defensin alpha 6
CD
1671
26891258, 19549264, 18305068
qPCR, Luciferase assays, Chromatin Immunoprecipitation assay, Immunohistochemistry, RT-PCR validation of selected Transcripts, Variability in gene expression profiles of two independent sets of UC RNA samples, Chromosomal locations of differentially expre
Human
Up
TREM1
Triggering receptor expressed on myeloid cells 1
IBD
54210
22721842, 21910175, 21763322, 18975078
ELISA, Westergren method, Trem-1 SNP and genotyping
Human
Up
CX3CL1
C-X3-C motif chemokine ligand 1
IBD
6376
17241867, 17285595
Taqman technology, qPCR, Stimulation of himec with cytokines, Leukocytes and CD40L, Flow cytometric using a coulter epics Xl flow cytometer (Beckman Coulter Inc., Fullerton, Ca), Characterization of himec and PBMC, Immunohistochemistry, Western blotting,
Human
Up
HORMAD2
HORMA domain containing 2
CD
150280
19915574
(GWAS) Selection of SNPS genotyping
Human
IBD4
Inflammatory bowel disease 4
CD
50608
10747815
Genotyping by Abi prism linkage mapping set version 2, IBD susceptibility genes
Human
MOCOS
Molybdenum cofactor sulfurase
CD
55034
19500084
Known SNPS in (Xdh, Mocos and Aox1) selected using the applied biosystems, Taqman SNP genotyping assays, qPCR, Sequencing by Beckman Coulter dye terminator sequencing kit
Human
MIF
Macrophage migration inhibitory factor
IBD, UC, CD
4282
24687413, 17206642, 18452219, 18023095, 12109441
RFLP-PCR, Genotyping, ELISA, RT-qPCR, Spectrophotometry, Western blot analysis, Cytokine assays, Flow cytometry
Human
MME
Membrane metallo-endopeptidase
IBD
4311
23827863
RNA isolation and qPCR, High-capacity cDNA reverse transcription kit, DNA isolation and genotyping
Immunohistochemistry and Image analyses, Immunostaining, ELISA, Immunoassay, Immunohistochemical studies of VEGF, SNPs analysis
Down
CFLAR
CASP8 and FADD like apoptosis regulator
UC, CD
8837
23371318, 16472594
Immunohistochemistry, IEC purity determination by RT-PCR, RT-qPCR, Antibodies, Immunoblotting, Chemiluminescence
Human
Up
IL17F
Interleukin 17F
UC, IBD
112744
17828618, 19263269, 18022867, 26558270
Genotyping of polymorphisms by PCR-SSCP method, One-tube multiplex PCR, PCR-RFLP
PTEN
Phosphatase and Tensin homolog
UC
5728
20067111, 23516074
Immunohistochemistry, Immunohistochemical detection, Western blot analysis, Tunel assay
female Balb/c mice
F9
Coagulation factor IX
CD
2158
29945876
DSS-Induced colitis model and tissue preparation, Immunoblotting, Myeloperoxidase activity assay, CXCL1 ELISA
C57BL/6J WT control mice (F9+/+), F9_/_ mice
IGF1
Insulin like growth factor 1
IBD, CD
3479
21287667, 14691340, 11914023, 19751734
Serum assays, ELISA method, Western immunoblotting, qPCR, Immunostaining
Human cohort
CASP3
Caspase 3
IBD, CD
836
24553140, 15479684
EBV-transformed B-cell lines, Taqman SNP genotyping assay, Immortalized macrophage progenitors, Cellular ATG16L1 cleavage assays, Image-based flow cytometry, Western blots and Caspase assays
Mice
S100A9
S100 calcium binding protein A9
IBD1, CD, UC
6280
25781366, 29115397, 28138990, 28735301
Measurement of fecal calprotectin by quantitative ELISA, Immunochromatographic technology, Quantitative fecal immunochemical test, Immunohistochemistry, Immunocytochemistry, Relationships between post operative endoscopic recurrence, Fcal and HSCRP levels
Human
FCGR3B
Fc fragment of IgG receptor IIIB
IBD, UC
2215
23917248, 23128233
(GWAS) Multiplex PCR, SNP genotype
Human
CD2
CD2 molecule
CD, UC
914
7680015
Immunohistological labeling, in vitro cell aggregation, Effect of blocking antibodies against surface adhesion molecules
Human
SRC
SRC Proto-oncogene, Non-receptor tyrosine kinase
UC
6714
8674385
Isolation of colonic epithelial cells and purification of RNA, Probes, Electroelution and Chromatography on an Elutip-D column, Northern Blotting of RNA, Slotblotting, Radioactively labeled probes
ELISA, Radioimmunoassay of stored serum, Erythrocyte sedimentation rate, BMI, Serum albumin and C_reactive protein concentrations and white blood cell counts were determined
Human
PI3
Peptidase inhibitor 3
UC, IBD
5266
29084078, 17200145
RNA extraction and RT-qPCR assays, Immunohistochemical analysis, ELISA
Genotyping using the sequenom mass array system (all genotypes on collections IBD-1 To -5 were generated), Determining haplotypes
PSMD4
Proteasome 26S subunit, Non-ATPase 4
IBD, UC
5710
14621278, 10807895
Immunohistochemical staining, A lowering in the inflammatory blood parameters ESR, CRP andorosomucoid was demonstrated, Antisecretory Factor, Preparation of AF and test of AF potency, Histopathological examination of rectal biopsies
Human
FCGR3A
Fc fragment of IgG receptor III A
IBD, CD, UC
2214
23917248, 29333082, 23128233, 21091999
ELISA, PCR-RFLP, SNP genotyping, PCR-based real-time invader assay
ITGAM
Integrin subunit alpha M
CD, UC, IBD
3684
9473377, 9355789
SNP genotyping, Flow cytometry triple fluorescence analysis
ELISA, DSS-induced colitis, Stained with Hematoxylin and Eosin, Immunohistochemistry
Female Balb/c mice
HLA-DRA
Major histocompatibility complex, Class II, DR alpha
UC, CD
3105
23128233, 19122664, 12073071
(GWAS) EQTL SNPS, Network tools grail and dapple, SNP analysis, All downstream genotyping done by SNPlex and Taqman technologies
VIM
Vimentin
CD, IBD
7431
21699783, 18626977, 2124983
Co-Immunoprecipitation, Genotyping by Taqman, SNP analysis, Immunofluorescence, Luciferase assay, Western blots, Hematoxylin and Eosin staining, Immunohistochemistry
Human
CD28
CD28 molecule
IBD
940
14518246
Immunohistochemistry
Human
CDKN1A
Cyclin dependent kinase inhibitor 1A
IBD, UC, CD
1026
18507080, 24760188, 15060836
RT-qPCR, Illumina mRNA microarray platform was used for mRNA microarray assays, Transfection of miR-Mimic and Inhibitors, Western blotting, Cell cycle analysis by flow cytometry, Luciferase reporter assays
Human
Up
CCDC122
Coiled-coil domain containing 122
CD
160857
22984114
(GWAS) Genotyping using high-throughput sequenom mass array platform, SNP analysis
Human
FAS
Fas cell surface death receptor
UC, CD, IBD
355
15637757, 16049281, 16856205
PCR, SNP analysis, DHPLC, Haematoxylin and Eosin staining, Immunoreactivity scores, Immunohistochemistry, Flow cytometry
Human
Up
FASN
Fatty acid synthase
IBD, UC
2194
16753600
Immunohistochemistry
Human
Up
JUN
Jun Proto-oncogene, AP-1 transcription factor subunit
IBD
3725
8674385
Cytoplasmic, Nuclear, Tumor suppressor genes proto-oncogene probes were used, Electro-elution and Chromatography on an Elutip-D column, Slot blotting and Northern blotting of RNA
RNeasy mini kit (Qiagen), qPCR, Genotyping and haplotype analysis
Human
Down
IRF1
Interferon regulatory factor 1
CD
3659
17213842
(GWAS) Genotyping using sequenom mass array 7K system and MALDI-TOF MS analysis
Human
TYK2
Tyrosine kinase 2
UC, CD
7297
25744728, 19653082
(GWAS) Genotyping via qPCR, SNPS of Tyk2 gene were calculated, PCR-RFLP, Hapmap
Human
ICAM3
Intercellular adhesion molecule 3
IBD, UC
3385
27552332, 10931137
RT-qPCR, RT2 profiler human tight junction PCR array (Qiagen #Pahs-143Zc-12) for mRNA expression analysis of samples, Quantitative direct sandwich ELISA
Human
Up
IL27
Interleukin 27
UC, IBD
246778
19686419, 19915574, 27221243
(GWAS) RT-PCR, Genotype analysis of the IL-27 gene was performed by the single-base extension method, Immunohistochemistry, Rt-qPCR, Ficoll reagent
Human
Up
TNFRSF6B
TNF receptor superfamily member 6b
IBD, UC, CD
8771
18758464, 23965943, 20675196
(GWAS) Genome-wide SNP genotyping using illumina infinium humanhap550 beadchip technolo, ELISA, Gene expression analyses using affymetrix genechip Hg-U133 plus 2.0 arrays, Fluorescent-automated DNA sequencing using the Qiagen fast cycling PCR kit, Infrare
Human
CCR6
C-C motif chemokine receptor 6
IBD, UC
1235
29981781, 26536229, 22269120
Flow cytometry, ELISA, Histological examination, Immunostaining and in situ hybridization, Transcriptome analysis and RT-qPCR confirmation, Immunohistochemistry, Genotyping by PCR-RFLP
Human
LTA
Lymphotoxin alpha
CD, UC
4049
16246225, 8668926, 16931032
PCR-RFLP, DNA extraction, analysis of the TNF-_ gene polymorphism, ELISA
Human
LTB
Lymphotoxin beta
UC, CD
4050
8608636, 8612993
Indirect immunofluorescence technique, PCR-RFLP, DNA extraction, FITC conjugate
Human
ST2
Suppression of tumorigenicity 2
IBD, UC
9173
20385815, 21633527
Flow cytometry FACS, Immunohistochemistry, Immunohistochemical staining, RT-PCR, Western blot analysis, Sandwich and multiplex ELISA kits
SAMP and AKR Mice, Human
IL-36A
Interleukin 36 alpha
UC
27179
26813344
qPCR, Immunohistochemistry, Flow cytometry FACS
il36r_/_ mice
PTGER4
Prostaglandin E receptor 4
IBD, CD
5734
20222910, 20846217, 24793213
(GWAS) Selection of SNP, Genotyping using the sequenom mass array system, qPCR
Human
TNFSF11
TNF superfamily member 11
CD
8600
20848544, 17663430
Measurement of OPG By ELISA
Human
MUC1
Mucin 1, Cell surface associated
IBD, CD
4585
19025220, 28885228, 11559653
Immunohistochemistry, ELISA, Hematoxylin and Eosin staining, Mucosal gene expression Study, RT-qPCR, Expression quantitative trait loci (EQTL) mapping
Immunohistochemistry, Western blot, Hematoxylin and Eosin techniques, Flow cytometry, FITC
Human
ZAP70
Zeta chain of T cell receptor associated protein kinase 70
UC, CD
7535
23406209
(GWAS) Mass spectrometric analysis (Iplex assay, Sequenom, San Diego, Ca) were used for genotyping on the sequenom mass array, Multiplex PCR, Spectrochip microarray, MALDI-TOF mass spectrometry
Human
CLEC2D
C-type lectin domain family 2 member D
IBD
29121
22664939
Genotyping for the SNPS was performed by PCR-RFLP
Human
RUNX3
RUNX family transcription factor 3
IBD
864
20887385, 18668679
(GWAS) Genotyping of all the SNP markers using Maldi_Tof MS sequenom�, qPCR, Immunohistochemical staining, Immunohistochemistry, mRNA by RT-PCR
Mice
Up
SERPINE1
Serpin family E member 1
UC, CD
5054
17111197, 24496159, 18844621, 12694086
Genotyping, Arms-PCR, Immunohistochemistry
Human
CD101
CD101 molecule
IBD
9398
26813346
Flow cytometry, Intracellular Ccytokine staining
Mice
NELL1
Neural EGFL like 1
CD, IBD
4745
17684544
SNP genotyping, RT-qPCR
Genome-wide case-control association
IBD6
Inflammatory bowel disease 6
IBD
50942
23071489
SNP-SNP interaction
Human cohort
IBD7
Inflammatory bowel disease7
IBD, CD
57042
23071489, 10814724, 20439597
SNP-SNP interaction, Serological testing
Human cohort
PRDM1
PR/SET domain 1
CD
639
23624108, 23028907
(GWAS) RT-qPCR, EQTL, Flow cytometry, SNP genotyping
Flow cytometry analysis, ELISA, Immunostaining and morphometric analysis of intestinal microvasculature, in vitro tube formation assay, DSS-induced colitis, Western blot and immunoprecipitation analysis, Histopathological analysis
Mice
IL10RB
Interleukin 10 receptor subunit beta
PIBD, CD
3588
28267044, 16537974, 22550014, 24379584
Sanger Sequencing, Western blotting, RT-PCR
Human, Mice
ITGAX
Integrin subunit alpha X
UC
3687
12610322, 10935652, 9473377
Spectrofluorometric, Immunohistochemical staining
Human
ITGAL
Integrin subunit alpha L
IBD
3683
11862384, 14518246, 10935652, 19340879, 12139949
SNP genotyping, Immunohistochemistry, Flow cytometry analysis, Immunofluorescent staining
Human
UP
IL15RA
Interleukin 15 receptor subunit alpha
IBD
3601
23039249, 23128233, 15770395
Immunohistochemistry and Immunofluorescence, ELISA, Spectrophotometer (Nanodrop technologies), RT-qPCR
Human
IL12RB2
Interleukin 12 receptor subunit beta 2
CD
3595
22412388, 12492197, 11120856, 23128233
(GWAS) SNP genotyping, Flow cytometry, RT-PCR
Human
IL-37
Interleukin 37
IBD
27178
25214710, 23600829
Immunohistochemistry, qPCR, Western blot, ELISA
UP
OSM
Oncostatin M
IBD
5008
28368383, 23128233
(GWAS) Genome wide association studies, qPCR, Flow cytometry analysis of human intestinal mucosa, ELISA, RNA extraction cDNA synthesis, Immunohistochemistry, Total protein extraction and Immunoblot analysis
C57BL/6 Mice
PUS10
Pseudouridine synthase 10
UC, CD
150962
23128233, 19068216, 20228799, 21298027
(GWAS) SNP genotyping, RT-PCR, Luciferase activity, ER-stress reporter, Immunostaining and fluorescence microscopy