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 Gene Rank Hugo description expected final
Results: HTML CSV LaTeX Showing element 2108 to 2157 of 3206 in total
measured
Rank
Hugo
description
expected
final
0.19122 2188 C12orf65 0.84475 0.226362829
0.191363 3032 UBE2E2 1.62653 0.117651073
0.191364 2850 TMEM33 DB83 PROTEIN. [SWISSPROT;Acc:P57088] 1 0.191364
0.191556 701 SYVN1 HRD1 PROTEIN ISOFORM A; SYNOVIOLIN1. [RefSeq;Acc:NM_032431] 0.722002 0.265312284
0.191835 1382 DDX55 0.784198 0.24462572
0.192159 22 NAV2 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 1924 POLR3C POLYMERASE (RNA) III (DNA DIRECTED) (62KD). [RefSeq;Acc:NM_006468] 0.828592 0.231957345
0.192216 2512 ILK 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 2433 IMMP1L 0.884993 0.217269515
0.192536 1682 NMNAT3 NICOTINAMIDE NUCLEOTIDE ADENYLYLTRANSFERASE 3; PYRIDINE NUCLEOTIDE ADENYLYLTRANSFERASE 3. [RefSeq;Acc:NM_178177] 0.808409 0.238166572
0.192847 747 CLUAP1 0.729107 0.264497529
0.192957 108 SCP2 "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 1445 QARS GLUTAMINYL-TRNA SYNTHETASE (EC 6.1.1.18) (GLUTAMINE--TRNA LIGASE) (GLNRS). [SWISSPROT;Acc:P47897] 0.793116 0.243459973
0.193159 899 SRP68 SIGNAL RECOGNITION PARTICLE 68 KDA PROTEIN (SRP68). [SWISSPROT;Acc:Q9UHB9] 0.744637 0.259400218
0.193284 1160 JPH4 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 2110 ZNRD1 "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 2796 PAK7 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 1834 C15orf15 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 230 no value JUN DIMERIZATION PROTEIN. [RefSeq;Acc:NM_130469] 0.614336 0.315215127
231 FOS PROTO-ONCOGENE PROTEIN C-FOS (CELLULAR ONCOGENE FOS) (G0/G1 SWITCH REGULATORY PROTEIN 7). [SWISSPROT;Acc:P01100]
0.193666 204 CRAT CARNITINE O-ACETYLTRANSFERASE (EC 2.3.1.7) (CARNITINE ACETYLASE) (CAT). [SWISSPROT;Acc:P43155] 0.601521 0.321960497
0.193703 2964 FOXP3 FORKHEAD BOX PROTEIN P3 (ZINC FINGER PROTEIN JM2) (SCURFIN). [SWISSPROT;Acc:Q9BZS1] 1.33367 0.145240577
0.194172 2489 no value 0.898593 0.216084479
0.194219 219 EIF3A EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 10 (EIF-3 THETA) (EIF3 P167) (EIF3 P180) (EIF3 P185) (EIF3A). [SWISSPROT;Acc:Q14152] 0.608459 0.319198171
220 EIF3G 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 2305 CNDP1 GLUTAMATE CARBOXYPEPTIDASE-LIKE PROTEIN 2 PRECURSOR. [SWISSPROT;Acc:Q96KN2] 0.875357 0.222216764
0.19466 915 IL4I1 INTERLEUKIN-4 INDUCED PROTEIN 1 PRECURSOR (FIG-1 PROTEIN). [SWISSPROT;Acc:Q96RQ9] 0.754632 0.257953546
0.195152 2488 FBLN2 FIBULIN-2 PRECURSOR. [SWISSPROT;Acc:P98095] 0.90295 0.216127139
0.195279 1534 ACO1 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 1691 NADK 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 2788 REEP5 POLYPOSIS LOCUS PROTEIN 1 (TB2 PROTEIN). [SWISSPROT;Acc:Q00765] 0.977987 0.199903475
0.196219 876 LSM5 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM5. [SWISSPROT;Acc:Q9Y4Y9] 0.754024 0.260229117
0.196655 2229 ATG12 AUTOPHAGY PROTEIN 12-LIKE (APG12-LIKE). [SWISSPROT;Acc:O94817] 0.876663 0.224322231
0.196675 907 NR6A1 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 1346 RAB3IL1 RAB3A INTERACTING PROTEIN (RABIN3)-LIKE 1. [RefSeq;Acc:NM_013401] 0.804471 0.245198397
0.197547 1883 CKMT2 "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 413 CCDC49 0.712745 0.27752422
0.198381 914 PRODH "PROLINE OXIDASE, MITOCHONDRIAL PRECURSOR (EC 1.5.3.-) (PROLINE DEHYDROGENASE). [SWISSPROT;Acc:O43272]" 0.768816 0.258034432
0.1984 806 GOSR2 27 KDA GOLGI SNARE PROTEIN (GOLGI SNAP RECEPTOR COMPLEX MEMBER 2) (MEMBRIN). [SWISSPROT;Acc:O14653] 0.757219 0.262011386
0.198456 2873 AGPAT2 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 845 ADCY6 "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 82 E2F1 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 367 HNRPF HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN F (HNRNP F). [SWISSPROT;Acc:P52597] 0.710442 0.279738529
0.198834 1137 PLSCR4 PHOSPHOLIPID SCRAMBLASE 4 (PL SCRAMBLASE 4) (CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 4). [SWISSPROT;Acc:Q9NRQ2] 0.793992 0.250423178
0.198895 641 TFCP2L1 LBP-9. [RefSeq;Acc:NM_014553] 0.741531 0.268222097
0.199227 1136 no value 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 575 BAAT BILE ACID COENZYME A: AMINO ACID N-ACYLTRANSFERASE; GLYCINE N-CHOLOYLTRANSFERASE. [RefSeq;Acc:NM_001701] 0.740509 0.270361333
0.200368 163 ZC3H14 NUCLEAR PROTEIN UKP68. [RefSeq;Acc:NM_024824] 0.582135 0.344195075
0.200609 1380 BAG1 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/