ModuleMiner   K.U.Leuven BioI@SISTA VIB


Input genes

Ensembl ID    Short name    Description
ENSG00000111964    APOM    Apolipoprotein M (Apo-M) (ApoM) (G3a protein). [Source:Uniprot/SWISSPROT;Acc:O95445]
ENSG00000131482    G6PC    Glucose-6-phosphatase (EC 3.1.3.9) (G6Pase) (G-6-Pase). [Source:Uniprot/SWISSPROT;Acc:P35575]
ENSG00000021852    C8B    Complement component C8 beta chain precursor (Complement component 8 beta subunit). [Source:Uniprot/SWISSPROT;Acc:P07358]
ENSG00000110245    APOC3    Apolipoprotein C-III precursor (Apo-CIII) (ApoC-III). [Source:Uniprot/SWISSPROT;Acc:P02656]
ENSG00000118271    TTR    Transthyretin precursor (Prealbumin) (TBPA) (TTR) (ATTR). [Source:Uniprot/SWISSPROT;Acc:P02766]
ENSG00000130707    ASS    Argininosuccinate synthase (EC 6.3.4.5) (Citrulline--aspartate ligase). [Source:Uniprot/SWISSPROT;Acc:P00966]
ENSG00000163631    ALB    Serum albumin precursor. [Source:Uniprot/SWISSPROT;Acc:P02768]
ENSG00000167711    SERPINF2    Alpha-2-antiplasmin precursor (Alpha-2-plasmin inhibitor) (Alpha-2-PI) (Alpha-2-AP). [Source:Uniprot/SWISSPROT;Acc:P08697]
ENSG00000124253    PCK1    Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) (Phosphoenolpyruvate carboxylase) (PEPCK-C). [Source:Uniprot/SWISSPROT;Acc:P35558]
ENSG00000021826    CPS1    Carbamoyl-phosphate synthase [ammonia], mitochondrial precursor (EC 6.3.4.16) (Carbamoyl-phosphate synthetase I) (CPSase I). [Source:Uniprot/SWISSPROT;Acc:P31327]
ENSG00000145321    GC    Vitamin D-binding protein precursor (DBP) (Group-specific component) (Gc-globulin) (VDB). [Source:Uniprot/SWISSPROT;Acc:P02774]
ENSG00000166308    C4A    Complement C4 precursor [Contains: Complement C4 beta chain; Complement C4 alpha chain; C4a anaphylatoxin; C4b; Complement C4 gamma chain]. [Source:Uniprot/SWISSPROT;Acc:P01028]
ENSG00000091583    APOH    Beta-2-glycoprotein I precursor (Apolipoprotein H) (Apo-H) (B2GPI) (Beta(2)GPI) (Activated protein C-binding protein) (APC inhibitor) (Anticardiolipin cofactor). [Source:Uniprot/SWISSPROT;Acc:P02749]
ENSG00000055957    ITIH1    Inter-alpha-trypsin inhibitor heavy chain H1 precursor (ITI heavy chain H1) (Inter-alpha-inhibitor heavy chain 1) (Inter-alpha-trypsin inhibitor complex component III) (Serum-derived hyaluronan-associated protein) (SHAP). [Source:Uniprot/SWISSPROT;Acc:P19827]


Input genes Gene Ontology overrepresented terms

GO ID    Description    Nr of annotated genes    p-value
GO:0005615    extracellular space    8 / 364    2.09E-7
GO:0005576    extracellular region    9 / 861    8.48E-6
GO:0044271    nitrogen compound biosynthesis    2 / 4    9.73E-4
GO:0006526    arginine biosynthesis    2 / 4    9.73E-4
GO:0000050    urea cycle    2 / 6    0.00218
GO:0005319    lipid transporter activity    3 / 51    0.00267
GO:0009308    amine metabolism    4 / 171    0.00375
GO:0006525    arginine metabolism    2 / 9    0.00491
GO:0000051    urea cycle intermediate metabolism    2 / 10    0.00605
GO:0009084    glutamine family amino acid biosynthesis    2 / 11    0.00732
GO:0004866    endopeptidase inhibitor activity    3 / 83    0.0112
GO:0030414    protease inhibitor activity    3 / 84    0.0116
GO:0006958    complement activation; classical pathway    2 / 16    0.0154
GO:0006952    defense response    5 / 520    0.0229
GO:0008652    amino acid biosynthesis    2 / 21    0.0265
GO:0006956    complement activation    2 / 23    0.0317
GO:0009064    glutamine family amino acid metabolism    2 / 24    0.0345
GO:0007582    physiological process    14 / 6754    0.0439
GO:0009607    response to biotic stimulus    5 / 602    0.0452


Input TFBS set

Sequences: human-mouse conserved non-coding sequences, 10 kb 5' of TSS, based on Ensembl 36 and selected using LAGAN (75 % identity over 100 bp) - to correct for possible differences in TSS, the mouse sequence was extended by 100kb in both directions for this alignment
Transcription factor binding site predictions: MotifScanner (prior = 0.2) - only binding sites were retained for transcription factors also showing binding sites on the orthologous mouse region


cis-regulatory module model cluster content

PWM    Weight
M00193-V$NF1_Q6    1.0
M00912-V$CEBP_Q2_01    0.989
M00158-V$COUP_01    0.989
MA0046-TCF1    0.668
M00762-V$DR1_Q3    0.658
M00763-V$PPAR_DR1_Q2    0.326
M00132-V$HNF1_01    0.204
M00483-V$ATF6_01    0.178
M00118-V$MYCMAX_01    0.168
M00119-V$MAX_01    0.163
M00790-V$HNF1_Q6    0.137
M00055-V$NMYC_01    0.0918
MA0101-REL    0.0612
M00615-V$MYCMAX_03    0.0561
MA0093-USF1    0.051
MA0059-MYC-MAX    0.0459
M00965-V$DR4_Q2    0.0357
M01031-V$HNF4_Q6_01    0.0306
M00053-V$CREL_01    0.0255
MA0058-MAX    0.0255
M00701-V$SMAD3_Q6    0.0255
M00470-V$AP2GAMMA_01    0.0153
M00211-V$PADS_C    0.0153
M00217-V$USF_C    0.0102
M00799-V$MYC_Q2    0.0051
M00220-V$SREBP1_01    0.0051
MA0004-Arnt    0.0051
M00469-V$AP2ALPHA_01    0.0051


cis-regulatory module model cluster content, grouping similar PWMs

PWM group    Weight
MA0046-TCF1,     M00790-V$HNF1_Q6,     M00132-V$HNF1_01    1.01
M00193-V$NF1_Q6    1.0
M00912-V$CEBP_Q2_01    0.989
M00158-V$COUP_01    0.989
M00762-V$DR1_Q3    0.658
M00119-V$MAX_01,     M00118-V$MYCMAX_01,     M00055-V$NMYC_01,     MA0059-MYC-MAX,     M00615-V$MYCMAX_03,     M00217-V$USF_C,     MA0058-MAX,     M00799-V$MYC_Q2,     M00220-V$SREBP1_01,     MA0004-Arnt    0.576
M00763-V$PPAR_DR1_Q2    0.326
Other    0.443


cis-regulatory modules

Rank    Ensembl ID    Position relative to transcription start site
2276    ENSG00000021826    -7554 -> -7257
4    ENSG00000021852    -2120 -> -2034
(613)    ENSG00000021852    -7489 -> -7210
7487    ENSG00000055957    -2119 -> -1982
855    ENSG00000091583    -6239 -> -6101
25    ENSG00000110245    -174 -> 48
15    ENSG00000111964    -202 -> 42
13    ENSG00000118271    -188 -> 12
(778)    ENSG00000124253    -1075 -> -936
11    ENSG00000124253    -257 -> 50
824    ENSG00000130707    -700 -> -598
3    ENSG00000131482    -337 -> 49
626    ENSG00000145321    -2020 -> -1885
30    ENSG00000163631    -172 -> -22
7    ENSG00000166308    -190 -> 50
14    ENSG00000167711    -336 -> -193

Cis-regulatory modules

Conservation in additional species

10 orthologs found in the database of dog-rat conserved non-coding sequences:

Human gene    Dog gene    Rank    Position relative to transcription start site
ENSG00000111964    ENSCAFG00000000598    7    -237 -> -44
ENSG00000166308    ENSCAFG00000000701    1172    -159 -> 50
ENSG00000145321    ENSCAFG00000002949    1564    -190 -> -92
ENSG00000163631    ENSCAFG00000003016    14    -294 -> 18
ENSG00000055957    ENSCAFG00000008867    5491    -126 -> 35
ENSG00000124253    ENSCAFG00000012065    1    -742 -> -367
ENSG00000118271    ENSCAFG00000018046    3    -237 -> -9
ENSG00000118271    ENSCAFG00000018046    (504)    -9684 -> -9555
ENSG00000021852    ENSCAFG00000018937    30    -2715 -> -2552
ENSG00000167711    ENSCAFG00000019240    5    -1433 -> -1250
ENSG00000130707    ENSCAFG00000019945    4728    -149 -> -5

=> 6 dog orthologs in top 10% (p = 1.46E-4)

Cis-regulatory modules

New target genes conserved in human-mouse-rat-dog

Rank    Ensembl ID    Short name    Description    Position relative to transcription start site
1    ENSG00000101323    HAO1    Hydroxyacid oxidase 1 (EC 1.1.3.15) (HAOX1) (Glycolate oxidase) (GOX). [Source:Uniprot/SWISSPROT;Acc:Q9UJM8]    -170 -> -53
2    ENSG00000163586    FABP1    Fatty acid-binding protein, liver (L-FABP). [Source:Uniprot/SWISSPROT;Acc:P07148]    -187 -> -14
3    ENSG00000145808    ADAMTS19    ADAMTS-19 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 19) (ADAM-TS 19) (ADAM-TS19). [Source:Uniprot/SWISSPROT;Acc:Q8TE59]    -846 -> -638
4    ENSG00000198209    NP_000583.2    complement component 4B preproprotein [Source:RefSeq_peptide;Acc:NP_001002029]    -139 -> 50
5    ENSG00000140718    Q9BVD9_HUMAN    FTO protein. [Source:Uniprot/SPTREMBL;Acc:Q9BVD9]    -4050 -> -3238
6    ENSG00000101981    F9    Coagulation factor IX precursor (EC 3.4.21.22) (Christmas factor) (Plasma thromboplastin component) (PTC) [Contains: Coagulation factor IXa light chain; Coagulation factor IXa heavy chain]. [Source:Uniprot/SWISSPROT;Acc:P00740]    -157 -> 45
7    ENSG00000096155    BAT3    Large proline-rich protein BAT3 (HLA-B-associated transcript 3) (G3). [Source:Uniprot/SWISSPROT;Acc:P46379]    -3224 -> -3020
8    ENSG00000156925    ZIC3    Zinc finger protein ZIC 3 (Zinc finger protein of the cerebellum 3). [Source:Uniprot/SWISSPROT;Acc:O60481]    -6329 -> -6111
9    ENSG00000145425    RPS3A    40S ribosomal protein S3a. [Source:Uniprot/SWISSPROT;Acc:P61247]    -94 -> 50
10    ENSG00000166949    SMAD3    Mothers against decapentaplegic homolog 3 (SMAD 3) (Mothers against DPP homolog 3) (Mad3) (hMAD-3) (JV15-2) (hSMAD3). [Source:Uniprot/SWISSPROT;Acc:P84022]    -3372 -> -3265
11    ENSG00000108753    TCF2    Hepatocyte nuclear factor 1-beta (HNF-1beta) (HNF-1B) (Variant hepatic nuclear factor 1) (VHNF1) (Homeoprotein LFB3) (Transcription factor 2) (TCF-2). [Source:Uniprot/SWISSPROT;Acc:P35680]    -385 -> 50
12    ENSG00000135100    TCF1    Hepatocyte nuclear factor 1-alpha (HNF-1A) (Liver-specific transcription factor LF-B1) (LFB1) (Transcription factor 1) (TCF-1). [Source:Uniprot/SWISSPROT;Acc:P20823]    -371 -> 50
13    ENSG00000197728    RPS26    40S ribosomal protein S26. [Source:Uniprot/SWISSPROT;Acc:P62854]    -3946 -> -3450
14    ENSG00000091138    SLC26A3    Chloride anion exchanger (DRA protein) (Down-regulated in adenoma) (Solute carrier family 26 member 3). [Source:Uniprot/SWISSPROT;Acc:P40879]    -243 -> 30
15    ENSG00000185551    NR2F2    COUP transcription factor 2 (COUP-TF2) (COUP-TF II) (Apolipoprotein AI regulatory protein 1) (ARP-1). [Source:Uniprot/SWISSPROT;Acc:P24468]    -560 -> 50
16    ENSG00000109819    PPARGC1A    Peroxisome proliferator activated receptor gamma coactivator 1 alpha (PPAR gamma coactivator-1 alpha) (PPARGC-1 alpha) (PGC-1 alpha) (Ligand effect modulator-6). [Source:Uniprot/SWISSPROT;Acc:Q9UBK2]    -1982 -> -1692
17    ENSG00000180921    NP_940890.1    null    -5593 -> -5403
18    ENSG00000021488    SLC7A9    B(0,+)-type amino acid transporter 1 (B(0,+)AT) (Glycoprotein- associated amino acid transporter b0,+AT1). [Source:Uniprot/SWISSPROT;Acc:P82251]    -77 -> 33
19    ENSG00000174807    CD248    tumor endothelial marker 1 precursor [Source:RefSeq_peptide;Acc:NP_065137]    -6132 -> -5684
20    ENSG00000180745    NP_689524.1    null    -126 -> 8
21    ENSG00000123561    SERPINA7    Thyroxine-binding globulin precursor (T4-binding globulin). [Source:Uniprot/SWISSPROT;Acc:P05543]    -1470 -> -1239
22    ENSG00000105855    ITGB8    Integrin beta-8 precursor. [Source:Uniprot/SWISSPROT;Acc:P26012]    -7764 -> -7225
23    ENSG00000164853    XP_496843.1    PREDICTED: similar to Uncx4.1 [Source:RefSeq_peptide_predicted;Acc:XP_496843]    -2448 -> -1855
24    ENSG00000138823    MTP    Microsomal triglyceride transfer protein large subunit precursor. [Source:Uniprot/SWISSPROT;Acc:P55157]    -153 -> 19
25    ENSG00000009954    BAZ1B    Bromodomain adjacent to zinc finger domain protein 1B (Williams-Beuren syndrome chromosome region 9 protein) (WBRS9) (Williams syndrome transcription factor) (hWALP2). [Source:Uniprot/SWISSPROT;Acc:Q9UIG0]    -511 -> 50
26    ENSG00000173253    DMRT2    Doublesex-and mab-3-related transcription factor 2 (Doublesex-like 2 protein) (DSXL-2). [Source:Uniprot/SWISSPROT;Acc:Q9Y5R5]    -7067 -> -6955
27    ENSG00000079335    CDC14A    Dual specificity protein phosphatase CDC14A (EC 3.1.3.48) (EC 3.1.3.16) (CDC14 cell division cycle 14 homolog A). [Source:Uniprot/SWISSPROT;Acc:Q9UNH5]    -3080 -> -2941
28    ENSG00000064835    POU1F1    Pituitary-specific positive transcription factor 1 (Pit-1) (Growth hormone factor 1) (GHF-1). [Source:Uniprot/SWISSPROT;Acc:P28069]    -9463 -> -9003
29    ENSG00000108039    XPNPEP1    Xaa-Pro aminopeptidase 1 (EC 3.4.11.9) (X-Pro aminopeptidase 1) (X- prolyl aminopeptidase 1, soluble) (Cytosolic aminopeptidase P) (Soluble aminopeptidase P) (sAmp) (Aminoacylproline aminopeptidase). [Source:Uniprot/SWISSPROT;Acc:Q9NQW7]    -5223 -> -4974
30    ENSG00000174279    EVX2    Homeobox even-skipped homolog protein 2 (EVX-2). [Source:Uniprot/SWISSPROT;Acc:Q03828]    -2121 -> -1885
31    ENSG00000148444    COMMD3    COMM domain containing protein 3 (Bup protein) (PIL protein). [Source:Uniprot/SWISSPROT;Acc:Q9UBI1]    -78 -> 50
32    ENSG00000186951    PPARA    Peroxisome proliferator activated receptor alpha (PPAR-alpha). [Source:Uniprot/SWISSPROT;Acc:Q07869]    -1395 -> -1059
33    ENSG00000174165    NP_997223.1    zinc finger, DHHC domain containing 24 [Source:RefSeq_peptide;Acc:NP_997223]    -9168 -> -8848
34    ENSG00000105825    TFPI2    Tissue factor pathway inhibitor 2 precursor (TFPI-2) (Placental protein 5) (PP5). [Source:Uniprot/SWISSPROT;Acc:P48307]    -6240 -> -6001
35    ENSG00000127928    GNGT1    Guanine nucleotide-binding protein G(T) gamma-T1 subunit (Transducin gamma chain). [Source:Uniprot/SWISSPROT;Acc:P63211]    -9761 -> -9513
36    ENSG00000139269    INHBE    Inhibin beta E chain precursor (Activin beta-E chain). [Source:Uniprot/SWISSPROT;Acc:P58166]    -3844 -> -3645
37    ENSG00000135298    BAI3    Brain-specific angiogenesis inhibitor 3 precursor. [Source:Uniprot/SWISSPROT;Acc:O60242]    -2847 -> -2610
38    ENSG00000168476    NP_079508.2    receptor expression enhancing protein 4 [Source:RefSeq_peptide;Acc:NP_079508]    -1947 -> -1728
39    ENSG00000148848    ADAM12    ADAM 12 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 12) (Meltrin alpha). [Source:Uniprot/SWISSPROT;Acc:O43184]    -3427 -> -2793
40    ENSG00000138069    RAB1A    Ras-related protein Rab-1A (YPT1-related protein). [Source:Uniprot/SWISSPROT;Acc:P62820]    -1334 -> -1176
41    ENSG00000116690    PRG4    proteoglycan 4 [Source:RefSeq_peptide;Acc:NP_005798]    -910 -> -497
42    ENSG00000139318    DUSP6    Dual specificity protein phosphatase 6 (EC 3.1.3.48) (EC 3.1.3.16) (Mitogen-activated protein kinase phosphatase 3) (MAP kinase phosphatase 3) (MKP-3) (Dual specificity protein phosphatase PYST1). [Source:Uniprot/SWISSPROT;Acc:Q16828]    -4504 -> -4327
43    ENSG00000166016    ABTB2    Ankyrin repeat and BTB/POZ domain containing protein 2. [Source:Uniprot/SWISSPROT;Acc:Q8N961]    -2157 -> -1916
44    ENSG00000168658    NP_659429.3    null    -2218 -> -2074
45    ENSG00000198933    NP_055541.1    ProSAPiP2 protein [Source:RefSeq_peptide;Acc:NP_055541]    -1989 -> -1832
46    ENSG00000137270    GCM1    Chorion-specific transcription factor GCMa (Glial cells missing homolog 1) (GCM motif protein 1) (hGCMa). [Source:Uniprot/SWISSPROT;Acc:Q9NP62]    -244 -> 43
47    ENSG00000116833    NR5A2    Orphan nuclear receptor NR5A2 (Alpha-1-fetoprotein transcription factor) (Hepatocytic transcription factor) (B1-binding factor) (hB1F) (CYP7A promoter binding factor). [Source:Uniprot/SWISSPROT;Acc:O00482]    -5380 -> -5144
48    ENSG00000180592    NP_997254.2    null    -5761 -> -5413
49    ENSG00000119508    NR4A3    Orphan nuclear receptor NR4A3 (Nuclear hormone receptor NOR-1) (Neuron-derived orphan receptor 1) (Mitogen-induced nuclear orphan receptor). [Source:Uniprot/SWISSPROT;Acc:Q92570]    -7429 -> -7119
50    ENSG00000150361    KLHL1    Kelch-like protein 1. [Source:Uniprot/SWISSPROT;Acc:Q9NR64]    -518 -> 50
51    ENSG00000117707    PROX1    Homeobox prospero-like protein PROX1 (PROX 1). [Source:Uniprot/SWISSPROT;Acc:Q92786]    -1612 -> -1180
52    ENSG00000171759    PAH    Phenylalanine-4-hydroxylase (EC 1.14.16.1) (PAH) (Phe-4- monooxygenase). [Source:Uniprot/SWISSPROT;Acc:P00439]    -3030 -> -2794
53    ENSG00000101306    MYLK2    Myosin light chain kinase 2, skeletal/cardiac muscle (EC 2.7.1.117) (MLCK2). [Source:Uniprot/SWISSPROT;Acc:Q9H1R3]    -9629 -> -9421
54    ENSG00000084093    REST    RE1-silencing transcription factor [Source:RefSeq_peptide;Acc:NP_005603]    -1975 -> -1754
55    ENSG00000080561    TRIM1_HUMAN    Midline 2 protein (Midline defect 2) (Tripartite motif protein 1) (Midin 2) (RING finger protein 60). [Source:Uniprot/SWISSPROT;Acc:Q9UJV3]    -3623 -> -3509
56    ENSG00000140836    ATBF1    Alpha-fetoprotein enhancer binding protein (AT motif-binding factor) (AT-binding transcription factor 1). [Source:Uniprot/SWISSPROT;Acc:Q15911]    -7043 -> -6309
57    ENSG00000070759    TESK2    Dual specificity testis-specific protein kinase 2 (EC 2.7.1.37) (EC 2.7.1.112) (Testicular protein kinase 2). [Source:Uniprot/SWISSPROT;Acc:Q96S53]    -355 -> -32
58    ENSG00000132763    NP_056321.1    null    -9130 -> -8807
59    ENSG00000101076    HNF4A    Hepatocyte nuclear factor 4-alpha (HNF-4-alpha) (Transcription factor HNF-4) (Transcription factor 14). [Source:Uniprot/SWISSPROT;Acc:P41235]    -6695 -> -6254
60    ENSG00000107874    CUEDC2    CUE domain containing 2 [Source:RefSeq_peptide;Acc:NP_076945]    -2318 -> -1967
61    ENSG00000131724    IL13RA1    Interleukin-13 receptor alpha-1 chain precursor (IL-13R-alpha-1) (IL- 13RA-1) (CD213a1 antigen). [Source:Uniprot/SWISSPROT;Acc:P78552]    -490 -> -336
62    ENSG00000198493    Q16473_HUMAN    XA protein. [Source:Uniprot/SPTREMBL;Acc:Q16473]    -2267 -> -2109
63    ENSG00000168263    KCNV2    Potassium voltage-gated channel subfamily V member 2 (Voltage-gated potassium channel subunit Kv8.2). [Source:Uniprot/SWISSPROT;Acc:Q8TDN2]    -8542 -> -8332
64    ENSG00000107611    CUBN    cubilin [Source:RefSeq_peptide;Acc:NP_001072]    -289 -> -91
65    ENSG00000011347    SYT7    Synaptotagmin-7 (Synaptotagmin VII) (SytVII). [Source:Uniprot/SWISSPROT;Acc:O43581]    -9589 -> -9412
66    ENSG00000148584    NP_620310.1    apobec-1 complementation factor isoform 1 [Source:RefSeq_peptide;Acc:NP_055391]    -174 -> 49
67    ENSG00000130300    PLVAP_HUMAN    Plasmalemma vesicle-associated protein (Plasmalemma vesicle protein 1) (PV-1) (Fenestrated-endothelial linked structure protein). [Source:Uniprot/SWISSPROT;Acc:Q9BX97]    -2122 -> -1981
68    ENSG00000040199    PHLPL_HUMAN    PH domain leucine-rich repeat protein phosphatase-like (EC 3.1.3.16). [Source:Uniprot/SWISSPROT;Acc:Q6ZVD8]    -3162 -> -2988
69    ENSG00000147144    NP_296375.1    null    -144 -> 38
70    ENSG00000181110    RGAG1    retrotransposon gag domain containing 1 [Source:RefSeq_peptide;Acc:NP_065820]    -2933 -> -2186
71    ENSG00000155313    USP25    Ubiquitin carboxyl-terminal hydrolase 25 (EC 3.1.2.15) (Ubiquitin thiolesterase 25) (Ubiquitin-specific processing protease 25) (Deubiquitinating enzyme 25) (USP on chromosome 21). [Source:Uniprot/SWISSPROT;Acc:Q9UHP3]    -873 -> -696
72    ENSG00000139540    SLC39A5    solute carrier family 39 (metal ion transporter), member 5 [Source:RefSeq_peptide;Acc:NP_775867]    -226 -> 34
73    ENSG00000159131    GART    Trifunctional purine biosynthetic protein adenosine-3 [Includes: Phosphoribosylamine--glycine ligase (EC 6.3.4.13) (GARS) (Glycinamide ribonucleotide synthetase) (Phosphoribosylglycinamide synthetase); Phosphoribosylformylglycinamidine cyclo-ligase (EC 6. [Source:Uniprot/SWISSPROT;Acc:P22102]    -152 -> 49
74    ENSG00000186479    NP_001025046.1    R7 binding protein [Source:RefSeq_peptide;Acc:NP_001025046]    -4427 -> -4107
75    ENSG00000129422    MTUS1    mitochondrial tumor suppressor 1 isoform 3 [Source:RefSeq_peptide;Acc:NP_001001927]    -2408 -> -2175
76    ENSG00000158528    PPP1R9A    Neurabin-1 (Neurabin-I) (Neural tissue-specific F-actin binding protein I) (Protein phosphatase 1 regulatory subunit 9A). [Source:Uniprot/SWISSPROT;Acc:Q9ULJ8]    -5495 -> -5307
77    ENSG00000112137    PHACTR1    Phosphatase and actin regulator 1. [Source:Uniprot/SWISSPROT;Acc:Q9C0D0]    -888 -> -602
78    ENSG00000165494    PCF11_HUMAN    Pre-mRNA cleavage complex II protein Pcf11 (Fragment). [Source:Uniprot/SWISSPROT;Acc:O94913]    -337 -> 50
79    ENSG00000148943    LIN7C    LIN-7 homolog C (LIN-7C) (Mammalian LIN-seven protein 3) (MALS-3) (Vertebrate LIN 7 homolog 3) (Veli-3 protein). [Source:Uniprot/SWISSPROT;Acc:Q9NUP9]    -8067 -> -7281
80    ENSG00000176201    GBA3    cytosolic beta-glucosidase [Source:RefSeq_peptide;Acc:NP_066024]    -7085 -> -6789
81    ENSG00000079215    SLC1A3    Excitatory amino acid transporter 1 (Sodium-dependent glutamate/aspartate transporter 1) (Glial glutamate transporter) (GLAST-1). [Source:Uniprot/SWISSPROT;Acc:P43003]    -5783 -> -4980
82    ENSG00000179148    ALOXE3    Epidermis-type lipoxygenase 3 (EC 1.13.11.-) (e-LOX-3). [Source:Uniprot/SWISSPROT;Acc:Q9BYJ1]    -1372 -> -1210
83    ENSG00000123364    HOXC13    Homeobox protein Hox-C13 (Hox-3G). [Source:Uniprot/SWISSPROT;Acc:P31276]    -2012 -> -1897
84    ENSG00000023516    AKAP11    A-kinase anchor protein 11 (Protein kinase A anchoring protein 11) (PRKA11) (A kinase anchor protein 220 kDa) (AKAP 220) (hAKAP220). [Source:Uniprot/SWISSPROT;Acc:Q9UKA4]    -462 -> -325
85    ENSG00000121152    BRRN1    Condensin complex subunit 2 (Barren homolog protein 1) (Chromosome- associated protein H) (hCAP-H) (XCAP-H homolog). [Source:Uniprot/SWISSPROT;Acc:Q15003]    -5198 -> -5070
86    ENSG00000102038    SMARCA1    Possible global transcription activator SNF2L1 (SWI/SNF related matrix associated actin dependent regulator of chromatin subfamily A member 1). [Source:Uniprot/SWISSPROT;Acc:P28370]    -2098 -> -1731
87    ENSG00000168955    NP_079071.1    transmembrane 4 L six family member 20 [Source:RefSeq_peptide;Acc:NP_079071]    -167 -> 11
88    ENSG00000084676    NCOA1    Nuclear receptor coactivator 1 (EC 2.3.1.48) (NCoA-1) (Steroid receptor coactivator-1) (SRC-1) (RIP160) (Hin-2 protein). [Source:Uniprot/SWISSPROT;Acc:Q15788]    -6955 -> -6562
89    ENSG00000025434    NR1H3    Oxysterols receptor LXR-alpha (Liver X receptor alpha) (Nuclear orphan receptor LXR-alpha). [Source:Uniprot/SWISSPROT;Acc:Q13133]    -578 -> -286
90    ENSG00000115592    PRKAG3    5'-AMP-activated protein kinase, gamma-3 subunit (AMPK gamma-3 chain) (AMPK gamma3). [Source:Uniprot/SWISSPROT;Acc:Q9UGI9]    -3356 -> -3114
91    ENSG00000185721    DRG1    Developmentally regulated GTP-binding protein 1 (DRG 1). [Source:Uniprot/SWISSPROT;Acc:Q9Y295]    -1528 -> -1305
92    ENSG00000196549    MME    Neprilysin (EC 3.4.24.11) (Neutral endopeptidase) (NEP) (Enkephalinase) (Common acute lymphocytic leukemia antigen) (CALLA) (Neutral endopeptidase 24.11) (CD10). [Source:Uniprot/SWISSPROT;Acc:P08473]    -665 -> -325
93    ENSG00000147099    HDAC8    Histone deacetylase 8 (HD8). [Source:Uniprot/SWISSPROT;Acc:Q9BY41]    -379 -> 46
94    ENSG00000143549    TPM3    Tropomyosin alpha 3 chain (Tropomyosin 3) (Tropomyosin gamma) (hTM5). [Source:Uniprot/SWISSPROT;Acc:P06753]    -3514 -> -3324
95    ENSG00000164627    CF102_HUMAN    Kinesin-like motor protein C6orf102. [Source:Uniprot/SWISSPROT;Acc:Q6ZMV9]    -60 -> 50
96    ENSG00000111799    COL12A1    Collagen alpha 1(XII) chain precursor. [Source:Uniprot/SWISSPROT;Acc:Q99715]    -553 -> -162
97    ENSG00000152022    LIX1L    null    -220 -> 50
98    ENSG00000107338    SHB    SHB (Src homology 2 domain containing) adaptor protein B [Source:RefSeq_peptide;Acc:NP_003019]    -3187 -> -2741
99    ENSG00000177189    RPS6KA3    Ribosomal protein S6 kinase alpha 3 (EC 2.7.1.37) (S6K-alpha 3) (90 kDa ribosomal protein S6 kinase 3) (p90-RSK 3) (Ribosomal S6 kinase 2) (RSK-2) (pp90RSK2) (Insulin-stimulated protein kinase 1) (ISPK-1). [Source:Uniprot/SWISSPROT;Acc:P51812]    -5357 -> -5143
100    ENSG00000104369    JPH1    Junctophilin-1 (Junctophilin type 1) (JP-1). [Source:Uniprot/SWISSPROT;Acc:Q9HDC5]    -3019 -> -2752

Cis-regulatory modules

GO ID    Description    Nr of annotated genes    p-value
GO:0004879    ligand-dependent nuclear receptor activity    6 / 28    0.00372
GO:0003707    steroid hormone receptor activity    6 / 28    0.00372
GO:0006631    fatty acid metabolism    6 / 40    0.0265
GO:0006355    regulation of transcription; DNA-dependent    25 / 633    0.0358


Contact

peter.vanloo<at>med.kuleuven.be

Manuscript

Van Loo P., Aerts S., Thienpont B., De Moor B., Moreau Y. & Marynen P. (2008). ModuleMiner: improved computational detection of cis-regulatory modules. Different modes of gene regulation in embryonic development and adult tissues? Genome Biology, 9:R66.


Peter Van Loo
Copyright © 2006 Katholieke Universiteit Leuven