Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Gene Rank final expected description measured Hugo
Results: HTML CSV LaTeX Showing element 1152 to 1201 of 3206 in total
Rank
final
expected
description
measured
Hugo
1152 0.249716819 0.228299 SPROUTY HOMOLOG 3 (SPRY-3). [SWISSPROT;Acc:O43610] 0.0570101 SPRY3
1153 0.249716548 0.289996 SPROUTY HOMOLOG 2 (SPRY-2). [SWISSPROT;Acc:O43597] 0.0724168 SPRY2
1154 0.249716516 0.225762 SPROUTY HOMOLOG 1 (SPRY-1) (FRAGMENT). [SWISSPROT;Acc:O43609] 0.0563765 SPRY1
1155 0.249661086 0.508241 0.126888 PAPLN
1156 0.249660202 0.164951 0.0411817 CYB5D2
1157 0.249618801 3.13091 PROTEASOME SUBUNIT BETA TYPE 3 (EC 3.4.25.1) (PROTEASOME THETA CHAIN) (PROTEASOME CHAIN 13) (PROTEASOME COMPONENT C10-II). [SWISSPROT;Acc:P49720] 0.781534 PSMB3
1158 0.249617256 1.17572 ADAPTER-RELATED PROTEIN COMPLEX 2 BETA 1 SUBUNIT (BETA-ADAPTIN) (PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN BETA SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 BETA LARGE CHAIN) (AP105B). [SWISSPROT;Acc:P21851] 0.29348 AP2B1
1159 0.249563625 0.22389 ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1C SUBUNIT (SIGMA-ADAPTIN 1C) (ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1C SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1C SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA- 1C SMALL CHAIN) (SIGMA 1C SUBUNIT OF AP-1 CL 0.0558748 AP1S3
1160 0.24956326 0.774489 ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 2 SUBUNIT (GAMMA2-ADAPTIN) (ADAPTOR PROTEIN COMPLEX AP-1 GAMMA-2 SUBUNIT) (G2AD). [SWISSPROT;Acc:O75843] 0.193284 JPH4
1161 0.249563039 0.512059 ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1B SUBUNIT (SIGMA-ADAPTIN 1B) (ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1B SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1B SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA- 1B SMALL CHAIN) (SIGMA 1B SUBUNIT OF AP-1 CL 0.127791 no value
1162 0.24956274 0.925078 ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT (GAMMA-ADAPTIN) (ADAPTOR PROTEIN COMPLEX AP-1 GAMMA-1 SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN GAMMA-1 SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 GAMMA-1 LARGE CHAIN). [SWISSPROT;Acc:O43747] 0.230865 AP1G1
1163 0.249561907 0.456524 ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT (SIGMA-ADAPTIN 1A) (ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1A SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1A SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA- 1A SMALL CHAIN) (CLATHRIN COAT ASSEMBLY PROT 0.113931 AP1S1
1164 0.249506702 1.25482 ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT (BETA-ADAPTIN 1) (ADAPTOR PROTEIN COMPLEX AP-1 BETA-1 SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN BETA SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 BETA LARGE CHAIN). [SWISSPROT;Acc:Q10567] 0.313086 AP1B1
1165 0.249415051 0.579965 "SH2 DOMAIN BINDING PROTEIN 1; TPR-CONTAINING, SH2-BINDING PHOSPHOPROTEIN. [RefSeq;Acc:NM_014633]" 0.144652 no value
1166 0.249397007 0.16302 HISTONE DEACETYLASE 11 (HD11). [SWISSPROT;Acc:Q96DB2] 0.0406567 HDAC11
1167 0.249396926 0.564193 "THIOREDOXIN, MITOCHONDRIAL PRECURSOR (MT-TRX) (THIOREDOXIN 2). [SWISSPROT;Acc:Q99757]" 0.140708 TXN2
1168 0.249396846 0.129486 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 2 (SMAD 2) (MOTHERS AGAINST DPP HOMOLOG 2) (MAD-RELATED PROTEIN 2) (HMAD-2) (JV18-1) (HSMAD2). [SWISSPROT;Acc:Q15796] 0.0322934 SMAD2
1169 0.249396799 0.130885 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 3 (SMAD 3) (MOTHERS AGAINST DPP HOMOLOG 3) (MAD3) (HMAD-3) (MMAD3) (JV15-2) (HSMAD3). [SWISSPROT;Acc:Q92940] 0.0326423 SMAD3
1170 0.249396763 0.29839 HEPATOCELLULAR CARCINOMA SUSCEPTIBILITY PROTEIN; X 003 PROTEIN; HDCMC29P; HSPC260; LIKELY ORTHOLOG OF MOUSE CD40 LIGAND-ACTIVATED SPECIFIC TRANSCRIPT 3 (CLAST3). [RefSeq;Acc:NM_020232] 0.0744175 TNFSF5IP1
1171 0.24939667 0.246217 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 9 (SMAD 9) (MOTHERS AGAINST DPP HOMOLOG 9) (SMAD9) (MADH6). [SWISSPROT;Acc:O15198] 0.0614057 SMAD9
1172 0.249396621 0.231281 ETHANOLAMINE KINASE-LIKE PROTEIN EKI2 (FLJ10761). [SWISSPROT;Acc:Q9NVF9] 0.0576807 ETNK2
1173 0.24939654 0.266132 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 5 (SMAD 5) (MOTHERS AGAINST DPP HOMOLOG 5) (SMAD5) (HSMAD5) (JV5-1). [SWISSPROT;Acc:Q99717] 0.0663724 SMAD5
1174 0.249396497 4.48631 COP9 CONSTITUTIVE PHOTOMORPHOGENIC HOMOLOG SUBUNIT 5; JUN ACTIVATION DOMAIN-BINDING PROTEIN. [RefSeq;Acc:NM_006837] 1.11887 COPS5
1175 0.24939644 0.291272 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 1 (SMAD 1) (MOTHERS AGAINST DPP HOMOLOG 1) (MAD-RELATED PROTEIN 1) (TRANSFORMING GROWTH FACTOR- BETA SIGNALING PROTEIN-1) (BSP-1) (HSMAD1) (JV4-1). [SWISSPROT;Acc:Q15797] 0.0726422 SMAD1
1176 0.249396272 0.161745 "COP9 SUBUNIT 6 (MOV34 HOMOLOG, 34 KD). [RefSeq;Acc:NM_006833]" 0.0403386 COPS6
1177 0.249396249 0.292836 ETHANOLAMINE KINASE (EC 2.7.1.82) (EKI). [SWISSPROT;Acc:Q9HBU6] 0.0730322 ETNK1
1178 0.249297262 0.556039 PROTEIN PHOSPHATASE 2C BETA ISOFORM (EC 3.1.3.16) (PP2C-BETA). [SWISSPROT;Acc:O75688] 0.138619 PPM1B
1179 0.249233063 0.288355 0.0718676 FAM58A
1180 0.249208445 0.996772 MYELIN GENE EXPRESSION FACTOR 2. [RefSeq;Acc:NM_016132] 0.248404 MYEF2
1181 0.248957645 3.75112 PROTEASOME SUBUNIT ALPHA TYPE 6 (EC 3.4.25.1) (PROTEASOME IOTA CHAIN) (MACROPAIN IOTA CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX IOTA CHAIN) (27 KDA PROSOMAL PROTEIN) (PROS-27) (P27K). [SWISSPROT;Acc:P34062] 0.93387 PSMA6
1182 0.24889872 1.28396 ARF GTPASE-ACTIVATING PROTEIN GIT1 (G PROTEIN-COUPLED RECEPTOR KINASE- INTERACTOR 1). [SWISSPROT;Acc:Q9Y2X7] 0.319576 GIT1
1183 0.248741855 0.761637 UBIQUITIN. [SWISSPROT;Acc:P02248] 0.189451 UBC
1184 0.248713943 0.206095 EPSIN 2 ISOFORM B; EPS15 BINDING PROTEIN. [RefSeq;Acc:NM_014964] 0.0512587 EPN2
1185 0.248669157 0.59173 "ACTIVIN A RECEPTOR, TYPE IC; ACTIVIN RECEPTOR-LIKE KINASE 7. [RefSeq;Acc:NM_145259]" 0.147145 ACVR1C
1186 0.24866856 0.605923 SERINE/THREONINE-PROTEIN KINASE RECEPTOR R2 PRECURSOR (EC 2.7.1.37) (SKR2) (ACTIVIN RECEPTOR-LIKE KINASE 4) (ALK-4) (ACTR-IB). [SWISSPROT;Acc:P36896] 0.150674 ACVR1B
1187 0.248667578 0.355368 NEURONAL CALCIUM SENSOR 1 (NCS-1) (FREQUENIN HOMOLOG) (FREQUENIN-LIKE PROTEIN) (FREQUENIN-LIKE UBIQUITOUS PROTEIN). [SWISSPROT;Acc:P36610] 0.0883685 FREQ
1188 0.248665413 0.74967 TGF-BETA RECEPTOR TYPE I PRECURSOR (EC 2.7.1.37) (TGFR-1) (TGF-BETA TYPE I RECEPTOR) (SERINE/THREONINE-PROTEIN KINASE RECEPTOR R4) (SKR4) (ACTIVIN RECEPTOR-LIKE KINASE 5) (ALK-5). [SWISSPROT;Acc:P36897] 0.186417 TGFBR1
1189 0.248602884 0.123075 PROBABLE CATION-TRANSPORTING ATPASE 1 (EC 3.6.1.-). [SWISSPROT;Acc:Q9NQ11] 0.0305968 ATP13A2
1190 0.248602303 1.49174 MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A (MAD2-LIKE 1) (HSMAD2). [SWISSPROT;Acc:Q13257] 0.37085 MAD2L1
1191 0.24860218 0.155349 TATA BOX BINDING PROTEIN (TRANSCRIPTION INITIATION FACTOR TFIID) (TATA-BOX FACTOR) (TATA SEQUENCE-BINDING PROTEIN) (TBP). [SWISSPROT;Acc:P20226] 0.0386201 TBP
1192 ATP13A4
1193 0.248566276 0.812918 PROTEASOME SUBUNIT BETA TYPE 6 PRECURSOR (EC 3.4.25.1) (PROTEASOME DELTA CHAIN) (MACROPAIN DELTA CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX DELTA CHAIN) (PROTEASOME SUBUNIT Y). [SWISSPROT;Acc:P28072] 0.202064 PSMB6
1194 0.248553487 2.7231 PROTEASOME SUBUNIT BETA TYPE 8 PRECURSOR (EC 3.4.25.1) (PROTEASOME COMPONENT C13) (MACROPAIN SUBUNIT C13) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C13). [SWISSPROT;Acc:P28062] 0.676836 no value
1195 0.248524151 0.651828 "COP9 COMPLEX SUBUNIT 4; LIKELY ORTHOLOG OF MOUSE COP9 (CONSTITUTIVE PHOTOMORPHOGENIC), SUBUNIT 4 (ARABIDOPSIS); COP9 (CONSTITUTIVE PHOTOMORPHOGENIC, ARABIDOPSIS, HOMOLOG) SUBUNIT 4. [RefSeq;Acc:NM_016129]" 0.161995 COPS4
1196 0.248495023 0.5927 DIHYDROPYRIMIDINE DEHYDROGENASE [NADP+] PRECURSOR (EC 1.3.1.2) (DPD) (DHPDHASE) (DIHYDROURACIL DEHYDROGENASE) (DIHYDROTHYMINE DEHYDROGENASE). [SWISSPROT;Acc:Q12882] 0.147283 no value
1197 0.248479589 0.452838 SYNTAXIN 10 (SYN10). [SWISSPROT;Acc:O60499] 0.112521 STX10
1198 0.248459779 0.362026 SYNTAXIN 6. [SWISSPROT;Acc:O43752] 0.0899489 STX6
1199 0.248355362 0.985475 KV CHANNEL INTERACTING PROTEIN 2 ISOFORM 4; A-TYPE POTASSIUM CHANNEL MODULATORY PROTEIN 2; CARDIAC VOLTAGE GATED POTASSIUM CHANNEL MODULATORY SUBUNIT. [RefSeq;Acc:NM_173193] 0.244748 KCNIP2
1200 0.24835342 1.00481 POTASSIUM CHANNEL-INTERACTING PROTEIN 4 ISOFORM 4; CALSENILIN-LIKE PROTEIN. [RefSeq;Acc:NM_147183] 0.249548 KCNIP4
1201 0.248349665 0.432185 0.107333 FAM40A

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/