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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measured Hugo Rank Gene description expected final
Results: HTML CSV LaTeX Showing element 2108 to 2157 of 3206 in total
measured
Hugo
Rank
description
expected
final
0.19122 C12orf65 2188 0.84475 0.226362829
0.191363 UBE2E2 3032 1.62653 0.117651073
0.191364 TMEM33 2850 DB83 PROTEIN. [SWISSPROT;Acc:P57088] 1 0.191364
0.191556 SYVN1 701 HRD1 PROTEIN ISOFORM A; SYNOVIOLIN1. [RefSeq;Acc:NM_032431] 0.722002 0.265312284
0.191835 DDX55 1382 0.784198 0.24462572
0.192159 NAV2 22 NEURON NAVIGATOR 2 ISOFORM L; RETINOIC ACID INDUCIBLE IN NEUROBLASTOMA; PORE MEMBRANE AND/OR FILAMENT INTERACTING LIKE PROTEIN 2; HELICASE HELAD1. [RefSeq;Acc:NM_145117] 0.404444 0.475118929
0.192198 POLR3C 1924 POLYMERASE (RNA) III (DNA DIRECTED) (62KD). [RefSeq;Acc:NM_006468] 0.828592 0.231957345
0.192216 ILK 2512 INTEGRIN-LINKED PROTEIN KINASE 1 (EC 2.7.1.-) (ILK-1) (59 KDA SERINE/THREONINE PROTEIN KINASE) (P59ILK). [SWISSPROT;Acc:Q13418] 0.894997 0.2147672
0.192282 IMMP1L 2433 0.884993 0.217269515
0.192536 NMNAT3 1682 NICOTINAMIDE NUCLEOTIDE ADENYLYLTRANSFERASE 3; PYRIDINE NUCLEOTIDE ADENYLYLTRANSFERASE 3. [RefSeq;Acc:NM_178177] 0.808409 0.238166572
0.192847 CLUAP1 747 0.729107 0.264497529
0.192957 SCP2 108 "NONSPECIFIC LIPID-TRANSFER PROTEIN, MITOCHONDRIAL PRECURSOR (NSL-TP) (STEROL CARRIER PROTEIN 2) (SCP-2) (STEROL CARRIER PROTEIN X) (SCP-X) (SCPX). [SWISSPROT;Acc:P22307]" 0.526194 0.366703155
0.193092 QARS 1445 GLUTAMINYL-TRNA SYNTHETASE (EC 6.1.1.18) (GLUTAMINE--TRNA LIGASE) (GLNRS). [SWISSPROT;Acc:P47897] 0.793116 0.243459973
0.193159 SRP68 899 SIGNAL RECOGNITION PARTICLE 68 KDA PROTEIN (SRP68). [SWISSPROT;Acc:Q9UHB9] 0.744637 0.259400218
0.193284 JPH4 1160 ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 2 SUBUNIT (GAMMA2-ADAPTIN) (ADAPTOR PROTEIN COMPLEX AP-1 GAMMA-2 SUBUNIT) (G2AD). [SWISSPROT;Acc:O75843] 0.774489 0.24956326
0.193407 ZNRD1 2110 "ZINC RIBBON DOMAIN CONTAINING, 1; TRANSCRIPTION-ASSOCIATED ZINC RIBBON PROTEIN; RNA POLYMERASE I SMALL SPECIFIC SUBUNIT RPA12. [RefSeq;Acc:NM_014596]" 0.847287 0.228266219
0.193542 PAK7 2796 SERINE/THREONINE-PROTEIN KINASE PAK 7 (EC 2.7.1.-) (P21-ACTIVATED KINASE 7) (PAK-7) (PAK-5). [SWISSPROT;Acc:Q9P286] 0.968184 0.199902085
0.193647 C15orf15 1834 RIBOSOMAL PROTEIN L24-LIKE; 60S RIBOSOMAL PROTEIN L30 ISOLOG; MY024 PROTEIN; HOMOLOG OF YEAST RIBOSOMAL LIKE PROTEIN 24. [RefSeq;Acc:NM_016304] 0.827963 0.23388364
0.193648 no value 230 JUN DIMERIZATION PROTEIN. [RefSeq;Acc:NM_130469] 0.614336 0.315215127
FOS 231 PROTO-ONCOGENE PROTEIN C-FOS (CELLULAR ONCOGENE FOS) (G0/G1 SWITCH REGULATORY PROTEIN 7). [SWISSPROT;Acc:P01100]
0.193666 CRAT 204 CARNITINE O-ACETYLTRANSFERASE (EC 2.3.1.7) (CARNITINE ACETYLASE) (CAT). [SWISSPROT;Acc:P43155] 0.601521 0.321960497
0.193703 FOXP3 2964 FORKHEAD BOX PROTEIN P3 (ZINC FINGER PROTEIN JM2) (SCURFIN). [SWISSPROT;Acc:Q9BZS1] 1.33367 0.145240577
0.194172 no value 2489 0.898593 0.216084479
0.194219 EIF3A 219 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 10 (EIF-3 THETA) (EIF3 P167) (EIF3 P180) (EIF3 P185) (EIF3A). [SWISSPROT;Acc:Q14152] 0.608459 0.319198171
EIF3G 220 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 4 (EIF-3 DELTA) (EIF3 P44) (EIF-3 RNA-BINDING SUBUNIT) (EIF3 P42) (EIF3G). [SWISSPROT;Acc:O75821]
0.194519 CNDP1 2305 GLUTAMATE CARBOXYPEPTIDASE-LIKE PROTEIN 2 PRECURSOR. [SWISSPROT;Acc:Q96KN2] 0.875357 0.222216764
0.19466 IL4I1 915 INTERLEUKIN-4 INDUCED PROTEIN 1 PRECURSOR (FIG-1 PROTEIN). [SWISSPROT;Acc:Q96RQ9] 0.754632 0.257953546
0.195152 FBLN2 2488 FIBULIN-2 PRECURSOR. [SWISSPROT;Acc:P98095] 0.90295 0.216127139
0.195279 ACO1 1534 IRON-RESPONSIVE ELEMENT BINDING PROTEIN 1 (IRE-BP 1) (IRON REGULATORY PROTEIN 1) (IRP1) (FERRITIN REPRESSOR PROTEIN) (ACONITATE HYDRATASE) (EC 4.2.1.3) (CITRATE HYDRO-LYASE) (ACONITASE). [SWISSPROT;Acc:P21399] 0.806892 0.242013801
0.195442 NADK 1691 PUTATIVE INORGANIC POLYPHOSPHATE/ATP-NAD KINASE (EC 2.7.1.23) (POLY(P)/ATP NAD KINASE). [SWISSPROT;Acc:O95544] 0.821038 0.238042575
0.195503 REEP5 2788 POLYPOSIS LOCUS PROTEIN 1 (TB2 PROTEIN). [SWISSPROT;Acc:Q00765] 0.977987 0.199903475
0.196219 LSM5 876 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM5. [SWISSPROT;Acc:Q9Y4Y9] 0.754024 0.260229117
0.196655 ATG12 2229 AUTOPHAGY PROTEIN 12-LIKE (APG12-LIKE). [SWISSPROT;Acc:O94817] 0.876663 0.224322231
0.196675 NR6A1 907 ORPHAN NUCLEAR RECEPTOR NR6A1 (GERM CELL NUCLEAR FACTOR) (GCNF) (RETINOID RECEPTOR-RELATED TESTIS SPECIFIC RECEPTOR) (RTR). [SWISSPROT;Acc:Q15406] 0.76137 0.258317244
0.197255 RAB3IL1 1346 RAB3A INTERACTING PROTEIN (RABIN3)-LIKE 1. [RefSeq;Acc:NM_013401] 0.804471 0.245198397
0.197547 CKMT2 1883 "CREATINE KINASE, SARCOMERIC MITOCHONDRIAL PRECURSOR (EC 2.7.3.2) (S- MTCK) (MIB-CK) (BASIC-TYPE MITOCHONDRIAL CREATINE KINASE). [SWISSPROT;Acc:P17540]" 0.848743 0.232752435
0.197804 CCDC49 413 0.712745 0.27752422
0.198381 PRODH 914 "PROLINE OXIDASE, MITOCHONDRIAL PRECURSOR (EC 1.5.3.-) (PROLINE DEHYDROGENASE). [SWISSPROT;Acc:O43272]" 0.768816 0.258034432
0.1984 GOSR2 806 27 KDA GOLGI SNARE PROTEIN (GOLGI SNAP RECEPTOR COMPLEX MEMBER 2) (MEMBRIN). [SWISSPROT;Acc:O14653] 0.757219 0.262011386
0.198456 AGPAT2 2873 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE BETA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 2) (1-AGPAT 2) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-BETA) (LPAAT-BETA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 2). [SWISSPROT;Acc:O15120] 1.05097 0.18883127
0.198584 ADCY6 845 "ADENYLATE CYCLASE, TYPE VI (EC 4.6.1.1) (ATP PYROPHOSPHATE-LYASE) (CA(2+)-INHIBITABLE ADENYLYL CYCLASE). [SWISSPROT;Acc:O43306]" 0.761721 0.260704379
0.198685 E2F1 82 TRANSCRIPTION FACTOR E2F1 (E2F-1) (RETINOBLASTOMA BINDING PROTEIN 3) (RBBP-3) (PRB-BINDING PROTEIN E2F-1) (PBR3) (RETINOBLASTOMA-ASSOCIATED PROTEIN 1) (RBAP-1). [SWISSPROT;Acc:Q01094] 0.505165 0.393307137
0.198738 HNRPF 367 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN F (HNRNP F). [SWISSPROT;Acc:P52597] 0.710442 0.279738529
0.198834 PLSCR4 1137 PHOSPHOLIPID SCRAMBLASE 4 (PL SCRAMBLASE 4) (CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 4). [SWISSPROT;Acc:Q9NRQ2] 0.793992 0.250423178
0.198895 TFCP2L1 641 LBP-9. [RefSeq;Acc:NM_014553] 0.741531 0.268222097
0.199227 no value 1136 PHOSPHOLIPID SCRAMBLASE 3 (PL SCRAMBLASE 3) (CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 3). [SWISSPROT;Acc:Q9NRY6] 0.79556 0.250423601
0.199469 1882 "CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL PRECURSOR (EC 2.7.3.2) (U- MTCK) (MIA-CK) (ACIDIC-TYPE MITOCHONDRIAL CREATINE KINASE). [SWISSPROT;Acc:P12532]" 0.856983 0.232757243
0.200205 BAAT 575 BILE ACID COENZYME A: AMINO ACID N-ACYLTRANSFERASE; GLYCINE N-CHOLOYLTRANSFERASE. [RefSeq;Acc:NM_001701] 0.740509 0.270361333
0.200368 ZC3H14 163 NUCLEAR PROTEIN UKP68. [RefSeq;Acc:NM_024824] 0.582135 0.344195075
0.200609 BAG1 1380 BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-1 (BCL-2 BINDING ATHANOGENE- 1) (BAG-1) (GLUCOCORTICOID RECEPTOR-ASSOCIATED PROTEIN RAP46). [SWISSPROT;Acc:Q99933] 0.819994 0.244646912

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/