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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description Gene Rank measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1501 to 1550 of 3206 in total
description
Rank
measured
expected
final
Hugo
DNAJ HOMOLOG SUBFAMILY B MEMBER 4 (HEAT SHOCK 40 KDA PROTEIN 1 HOMOLOG) (HEAT SHOCK PROTEIN 40 HOMOLOG) (HSP40 HOMOLOG). [SWISSPROT;Acc:Q9UDY4] 969 0.0721855 0.282461 0.255559175 DNAJB4
DNAJ HOMOLOG SUBFAMILY B MEMBER 5 (HEAT SHOCK PROTEIN HSP40-3) (HEAT SHOCK PROTEIN COGNATE 40) (HSC40) (HSP40-2). [SWISSPROT;Acc:O75953] 968 DNAJB5
DOC-1 RELATED PROTEIN (DOC-1R). [SWISSPROT;Acc:O75956] 3101 0.247158 2.67998 0.092223823 CDK2AP2
DOCKING PROTEIN 1 (P62(DOK)) (DOWNSTREAM OF TYROSINE KINASE 1) (PP62). [SWISSPROT;Acc:Q99704] 29 0.0754466 0.177056 0.426117161 DOK1
DOCKING PROTEIN 2 (P56(DOK-2)) (DOWNSTREAM OF TYROSINE KINASE 2). [SWISSPROT;Acc:O60496] 26 0.0954445 0.223986 0.42611815 DOK2
DOK-LIKE PROTEIN. [RefSeq;Acc:NM_024872] 28 0.0753031 0.176719 0.426117735 no value
DOLICHOL-PHOSPHATE MANNOSYLTRANSFERASE (EC 2.4.1.83) (DOLICHOL- PHOSPHATE MANNOSE SYNTHASE) (DOLICHYL-PHOSPHATE BETA-D- MANNOSYLTRANSFERASE) (MANNOSE-P-DOLICHOL SYNTHASE) (MPD SYNTHASE) (DPM SYNTHASE). [SWISSPROT;Acc:O60762] 2829 0.349731 1.80836 0.193396779 DPM1
DOLICHYL-DIPHOSPHOOLIGOSACCHARIDE--PROTEIN GLYCOSYLTRANSFERASE 48 KDA SUBUNIT PRECURSOR (EC 2.4.1.119) (OLIGOSACCHARYL TRANSFERASE 48 KDA SUBUNIT) (DDOST 48 KDA SUBUNIT). [SWISSPROT;Acc:P39656] 2999 0.0217044 0.160664 0.135091869 DDOST
DOPACHROME TAUTOMERASE PRECURSOR (EC 5.3.3.12) (DT) (DCT) (DOPACHROME DELTA-ISOMERASE) (TYROSINASE-RELATED PROTEIN 2) (TRP-2) (TRP2). [SWISSPROT;Acc:P40126] 1134 0.10083 0.402579 0.250460158 DCT
DOUBLE-STRAND BREAK REPAIR PROTEIN MRE11A (MRE11 HOMOLOG 1). [SWISSPROT;Acc:P49959] 3028 0.121552 1.02221 0.118910987 MRE11A
DOUBLECORTIN (LISSENCEPHALIN-X) (LIS-X) (DOUBLIN). [SWISSPROT;Acc:O43602] 1401 0.303311 1.24261 0.244091871 DCX
DOWN-REGULATED IN METASTASIS. [RefSeq;Acc:NM_014503] 1526 1.17672 4.8561 0.242317909 UTP20
DPY-30-LIKE PROTEIN. [SWISSPROT;Acc:Q9C005] 768 0.3486 1.32226 0.263639526 no value
DR1-ASSOCIATED PROTEIN 1; NEGATIVE COFACTOR 2 ALPHA; DR1-ASSOCIATED COREPRESSOR. [RefSeq;Acc:NM_006442] 217 0.215654 0.675264 0.319362501 DRAP1
DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1 (EC 2.7.1.-) (MAP KINASE KINASE 1) (MAPKK 1) (ERK ACTIVATOR KINASE 1) (MAPK/ERK KINASE 1) (MEK1). [SWISSPROT;Acc:Q02750] 570 0.251342 0.928542 0.270684579 MAP2K1
DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 2 (EC 2.7.1.-) (MAP KINASE KINASE 2) (MAPKK 2) (ERK ACTIVATOR KINASE 2) (MAPK/ERK KINASE 2) (MEK2). [SWISSPROT;Acc:P36507] 569 MAP2K2
DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 3 (EC 2.7.1.-) (MAP KINASE KINASE 3) (MAPKK 3) (MAPK/ERK KINASE 3). [SWISSPROT;Acc:P46734] 2616 0.127536 0.605166 0.210745481 MAP2K3
DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 4 (EC 2.7.1.-) (MAP KINASE KINASE 4) (JNK ACTIVATING KINASE 1) (C-JUN N- TERMINAL KINASE KINASE 1) (JNKK) (SAPK/ERK KINASE 1) (SEK1). [SWISSPROT;Acc:P45985] 327 0.10034 0.351521 0.285445251 MAP2K4
DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 6 (EC 2.7.1.-) (MAP KINASE KINASE 6) (MAPKK 6) (MAPK/ERK KINASE 6) (SAPKK3). [SWISSPROT;Acc:P52564] 2617 0.143053 0.679075 0.210658617 MAP2K6
DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7 (EC 2.7.1.-) (MAP KINASE KINASE 7) (MAPKK 7) (MAPK/ERK KINASE 7) (JNK ACTIVATING KINASE 2) (C-JUN N-TERMINAL KINASE KINASE 2) (JNK KINASE 2) (JNKK 2). [SWISSPROT;Acc:O14733] 480 0.209195 0.762639 0.274304094 MAP2K7
DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A (EC 2.7.1.-) (PROTEIN KINASE MINIBRAIN HOMOLOG) (MNBH) (HP86) (DUAL SPECIFICITY YAK1-RELATED KINASE). [SWISSPROT;Acc:Q13627] 348 0.135144 0.478436 0.282470383 DYRK1A
DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1B (EC 2.7.1.-) (MIRK PROTEIN KINASE). [SWISSPROT;Acc:Q9Y463] 346 0.1052 0.372425 0.282472981 DYRK1B
DYMECLIN. [RefSeq;Acc:NM_017653] 558 0.50366 1.85853 0.270999123 DYM
DYNACTIN 4. [RefSeq;Acc:NM_032486] 1865 0.0462274 0.198227 0.233204357 DCTN5
DYNACTIN COMPLEX 50 KDA SUBUNIT (50 KDA DYNEIN-ASSOCIATED POLYPEPTIDE) (DYNAMITIN) (DCTN-50) (DYNACTIN 2). [SWISSPROT;Acc:Q13561] 1694 0.375423 1.57827 0.237869946 DCTN2
DYNAMIN 1-LIKE PROTEIN ISOFORM 3; DYNAMIN-LIKE PROTEIN. [RefSeq;Acc:NM_005690] 880 0.121609 0.467587 0.260077804 DNM1L
DYNEIN LIGHT CHAIN 2. [RefSeq;Acc:NM_080677] 930 0.266007 1.03319 0.257461841 DYNLL2
DYSKERIN (NUCLEOLAR PROTEIN NAP57) (CBF5 HOMOLOG). [SWISSPROT;Acc:O60832] 2603 0.95535 4.50581 0.212026251 DKC1
DYSTROBREVIN ALPHA (DYSTROBREVIN-ALPHA). [SWISSPROT;Acc:Q9Y4J8] 1222 0.762918 3.07607 0.248017113 DTNA
DYSTROBREVIN BETA (BETA-DYSTROBREVIN) (DTN-B). [SWISSPROT;Acc:O60941] 1209 0.86712 3.49509 0.248096616 DTNB
DYSTROBREVIN BINDING PROTEIN 1; DYSBINDIN. [RefSeq;Acc:NM_032122] 342 0.137665 0.484315 0.284246823 DTNBP1
DYSTROPHIN. [SWISSPROT;Acc:P11532] 1213 0.0802494 0.323509 0.24805925 no value
E-1 ENZYME. [RefSeq;Acc:NM_021204] 2451 0.175357 0.808504 0.216890702 ENOPH1
E1A BINDING PROTEIN P400; P400 SWI2/SNF2-RELATED PROTEIN; CAGH32 PROTEIN; TRINUCLEOTIDE REPEAT CONTAINING 12. [RefSeq;Acc:NM_015409] 465 0.0869671 0.315578 0.275580364 EP400
E1B-55KDA-ASSOCIATED PROTEIN 5 ISOFORM A. [RefSeq;Acc:NM_007040] 2133 0.0829182 0.363712 0.227977631 HNRPUL1
E2A-PBX1-ASSOCIATED PROTEIN; PUTATIVE 47 KDA PROTEIN. [RefSeq;Acc:NM_020140] 19 0.310118 0.652691 0.475137546 ANKS1B
EAP30 SUBUNIT OF ELL COMPLEX. [RefSeq;Acc:NM_007241] 1734 0.04274 0.180308 0.237038845 SNF8
EBP50-PDZ INTERACTOR OF 64 KDA (EPI64 PROTEIN). [SWISSPROT;Acc:Q9BXI6] 1027 0.2166 0.854644 0.253438859 TBC1D10A
ECOTROPIC VIRAL INTEGRATION SITE 5; NEUROBLASTOMA STAGE 4S GENE. [RefSeq;Acc:NM_005665] 1292 0.0317084 0.128948 0.245900673 EVI5
EH-DOMAIN CONTAINING PROTEIN 1 (TESTILIN) (HPAST1). [SWISSPROT;Acc:Q9H4M9] 2686 0.121 0.580932 0.208285996 EHD1
EH-DOMAIN CONTAINING PROTEIN 2. [SWISSPROT;Acc:Q9NZN4] 2689 0.0892656 0.428577 0.208283692 EHD2
EH-DOMAIN CONTAINING PROTEIN 3. [SWISSPROT;Acc:Q9NZN3] 2687 0.107786 0.517492 0.208285345 EHD3
EH-DOMAIN CONTAINING PROTEIN 4 (EH DOMAIN-CONTAINING PROTEIN FKSG7) (HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN 10/11). [SWISSPROT;Acc:Q9H223] 2688 0.0943663 0.453066 0.208283782 EHD4
EIF-5A2 PROTEIN. [RefSeq;Acc:NM_020390] 1588 0.326192 1.35491 0.240748094 EIF5A2
ELAC HOMOLOG 2; PUTATIVE PROSTATE CANCER SUSCEPTIBILITY PROTEIN; ELAC (E. COLI) HOMOLOG 2. [RefSeq;Acc:NM_018127] 1409 0.0575359 0.235798 0.244005038 ELAC2
ELAV-LIKE PROTEIN 1 (HU-ANTIGEN R) (HUR). [SWISSPROT;Acc:Q15717] 566 0.449826 1.66144 0.270744655 ELAVL1
ELAV-LIKE PROTEIN 2 (HU-ANTIGEN B) (HUB) (ELAV-LIKE NEURONAL PROTEIN 1) (NERVOUS SYSTEM-SPECIFIC RNA BINDING PROTEIN HEL-N1). [SWISSPROT;Acc:Q12926] 574 0.495602 1.83168 0.270572371 ELAVL2
ELAV-LIKE PROTEIN 3 (HU-ANTIGEN C) (HUC) (PARANEOPLASTIC CEREBELLAR DEGENERATION-ASSOCIATED ANTIGEN) (PARANEOPLASTIC LIMBIC ENCEPHALITIS ANTIGEN 21). [SWISSPROT;Acc:Q14576] 560 0.539175 1.99055 0.270867348 no value
ELAV-LIKE PROTEIN 4 (PARANEOPLASTIC ENCEPHALOMYELITIS ANTIGEN HUD) (HU-ANTIGEN D). [SWISSPROT;Acc:P26378] 572 0.495507 1.83073 0.270660884 ELAVL4
ELECTRON TRANSFER FLAVOPROTEIN BETA-SUBUNIT (BETA-ETF). [SWISSPROT;Acc:P38117] 2754 0.429899 2.11091 0.203655769 ETFB

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/