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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expected Gene Rank measured description final Hugo
Results: HTML CSV LaTeX Showing element 1952 to 2001 of 3206 in total
expected
Rank
measured
description
final
Hugo
0.752124 1087 0.189368 0.251777632 RPAP3
0.752395 1665 0.179673 "NUCLEAR INHIBITOR OF PROTEIN PHOSPHATASE-1 (NIPP-1) (PROTEIN PHOSPHATASE 1, REGULATORY INHIBITOR SUBUNIT 8) [INCLUDES: ACTIVATOR OF RNA DECAY (EC 3.1.4.-) (ARD-1)]. [SWISSPROT;Acc:Q12972]" 0.238801427 PPP1R8
0.753056 2790 0.150538 POLYPOSIS LOCUS PROTEIN 1-LIKE 1; LIKELY ORTHOLOG OF MOUSE POLYPOSIS LOCUS PROTEIN 1-LIKE 1. [RefSeq;Acc:NM_138393] 0.199902796 REEP6
0.753541 1102 0.189161 "PROTEIN KINASE, INTERFERON-INDUCIBLE DOUBLE STRANDED RNA DEPENDENT ACTIVATOR; PROTEIN ACTIVATOR OF THE INTERFERON-INDUCED PROTEIN KINASE. [RefSeq;Acc:NM_003690]" 0.251029473 PRKRAP1
0.75356 2615 0.159172 "EXPORTIN 1; EXPORTIN-1 (REQUIRED FOR CHROMOSOME REGION MAINTENANCE); EXPORTIN 1 (CRM1, YEAST, HOMOLOG); CRM1, YEAST, HOMOLOG. [RefSeq;Acc:NM_003400]" 0.211226711 XPO1
0.753661 1460 0.183187 ALPHA ADDUCIN (ERYTHROCYTE ADDUCIN ALPHA SUBUNIT). [SWISSPROT;Acc:P35611] 0.243062862 ADD1
0.754024 876 0.196219 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM5. [SWISSPROT;Acc:Q9Y4Y9] 0.260229117 LSM5
0.754632 915 0.19466 INTERLEUKIN-4 INDUCED PROTEIN 1 PRECURSOR (FIG-1 PROTEIN). [SWISSPROT;Acc:Q96RQ9] 0.257953546 IL4I1
0.755227 222 0.240086 SAD1/UNC-84 PROTEIN-LIKE 1. [SWISSPROT;Acc:O94901] 0.317899122 UNC84A
0.755771 1456 0.183757 GAMMA ADDUCIN (ADDUCIN-LIKE PROTEIN 70). [SWISSPROT;Acc:Q9UEY8] 0.243138464 ADD3
0.756337 297 0.227252 ATROPHIN-1 INTERACTING PROTEIN 1; ACTIVIN RECEPTOR INTERACTING PROTEIN 1; LIKELY ORTHOLOG OF MOUSE ACTIVIN RECEPTOR INTERACTING PROTEIN 1; ATROPHIN-1 INTERACTING PROTEIN A; MEMBRANE ASSOCIATED GUANYLATE KINASE 2; ACTIVIN RECEPTOR INTERACTING P. [Re 0.300463947 MAGI2
0.756695 2756 0.153382 0.202699899 ATAD1
0.757219 806 0.1984 27 KDA GOLGI SNARE PROTEIN (GOLGI SNAP RECEPTOR COMPLEX MEMBER 2) (MEMBRIN). [SWISSPROT;Acc:O14653] 0.262011386 GOSR2
0.75755 2810 0.149456 TUMOR PROTEIN D54 (HD54) (D52-LIKE 2). [SWISSPROT;Acc:O43399] 0.197288628 TPD52L2
0.757899 658 0.20255 U2 SMALL NUCLEAR RIBONUCLEOPROTEIN AUXILIARY FACTOR 35 KDA SUBUNIT RELATED-PROTEIN 1. [SWISSPROT;Acc:Q15695] 0.267251969 no value
0.758752 336 0.216233 HISTONE ACETYLTRANSFERASE TYPE B SUBUNIT 2 (RETINOBLASTOMA BINDING PROTEIN P46) (RETINOBLASTOMA-BINDING PROTEIN 7) (RBBP-7). [SWISSPROT;Acc:Q16576] 0.284985081 RBBP7
0.759373 2105 0.173405 UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANSFERASE 110 KDA SUBUNIT (EC 2.4.1.-) (O-GLCNAC TRANSFERASE P110 SUBUNIT). [SWISSPROT;Acc:O15294] 0.228352865 OGT
0.760447 1735 0.180241 RAD54-LIKE PROTEIN; RAD54 HOMOLOG. [RefSeq;Acc:NM_003579] 0.237019805 RAD54L
0.760495 60 0.312681 CELLULAR REPRESSOR OF E1A-STIMULATED GENES. [RefSeq;Acc:NM_003851] 0.411154577 CREG1
61 PUTATIVE ADENOSYLHOMOCYSTEINASE 3 (EC 3.3.1.1) (S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:Q96HN2] no value
0.76137 907 0.196675 ORPHAN NUCLEAR RECEPTOR NR6A1 (GERM CELL NUCLEAR FACTOR) (GCNF) (RETINOID RECEPTOR-RELATED TESTIS SPECIFIC RECEPTOR) (RTR). [SWISSPROT;Acc:Q15406] 0.258317244 NR6A1
0.761637 1183 0.189451 UBIQUITIN. [SWISSPROT;Acc:P02248] 0.248741855 UBC
0.761721 845 0.198584 "ADENYLATE CYCLASE, TYPE VI (EC 4.6.1.1) (ATP PYROPHOSPHATE-LYASE) (CA(2+)-INHIBITABLE ADENYLYL CYCLASE). [SWISSPROT;Acc:O43306]" 0.260704379 ADCY6
0.762639 480 0.209195 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] 0.274304094 MAP2K7
0.765015 649 0.204901 RETINOIC ACID INDUCED 17; PIAS-LIKE PROTEIN HZIMP10. [RefSeq;Acc:NM_020338] 0.267839193 ZMIZ1
0.766097 2560 0.16418 AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY A MEMBER 1 (NEURON- SPECIFIC X11 PROTEIN) (NEURONAL MUNC18-1-INTERACTING PROTEIN 1) (MINT-1) (ADAPTER PROTEIN X11ALPHA). [SWISSPROT;Acc:Q02410] 0.214307066 APBA1
0.766628 1556 0.184977 0.241286517 no value
0.766919 416 0.212723 CLATHRIN COAT ASSEMBLY PROTEIN AP180 (CLATHRIN COAT ASSOCIATED PROTEIN AP180) (91 KDA SYNAPTOSOMAL-ASSOCIATED PROTEIN). [SWISSPROT;Acc:O60641] 0.277373491 SNAP91
0.767511 1971 0.177407 60S RIBOSOMAL PROTEIN L30. [SWISSPROT;Acc:P04645] 0.231145873 RPL30
0.768033 1711 0.18248 0.237593958 PNPLA7
0.768755 1353 0.188445 RING FINGER PROTEIN 20. [RefSeq;Acc:NM_019592] 0.245130113 RNF20
1354 RING FINGER PROTEIN 40; 95 KDA RETINOBLASTOMA PROTEIN BINDING PROTEIN; LIKELY ORTHOLOG OF RAT STARING. [RefSeq;Acc:NM_014771] RNF40
0.768816 914 0.198381 "PROLINE OXIDASE, MITOCHONDRIAL PRECURSOR (EC 1.5.3.-) (PROLINE DEHYDROGENASE). [SWISSPROT;Acc:O43272]" 0.258034432 PRODH
0.768853 185 0.253477 SIMILAR TO LIM DOMAIN ONLY 7 (FRAGMENT). [SPTREMBL;Acc:Q8N6M2] 0.329682007 LIMCH1
0.768906 2487 0.166202 0.21615386 GLT25D1
0.770597 72 0.31296 "DELTA3,5-DELTA2,4-DIENOYL-COA ISOMERASE, MITOCHONDRIAL PRECURSOR (EC 5.3.3.-). [SWISSPROT;Acc:Q13011]" 0.406126678 ECH1
0.771779 3122 0.0676858 CARTILAGE OLIGOMERIC MATRIX PROTEIN PRECURSOR (COMP). [SWISSPROT;Acc:P49747] 0.087701013 COMP
0.772261 3187 0.028817 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14C; SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-81; PKC-POTENTIATED PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_030949]" 0.037315105 no value
0.773023 1811 0.18122 AMINOACYLASE-1 (EC 3.5.1.14) (N-ACYL-L-AMINO-ACID AMIDOHYDROLASE) (ACY-1). [SWISSPROT;Acc:Q03154] 0.234430282 ACY1
0.774489 1160 0.193284 ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 2 SUBUNIT (GAMMA2-ADAPTIN) (ADAPTOR PROTEIN COMPLEX AP-1 GAMMA-2 SUBUNIT) (G2AD). [SWISSPROT;Acc:O75843] 0.24956326 JPH4
0.775204 3121 0.0679913 THROMBOSPONDIN 3 PRECURSOR. [SWISSPROT;Acc:P49746] 0.087707623 THBS3
0.775495 53 0.318849 DISKS LARGE-ASSOCIATED PROTEIN 2 (DAP-2) (SAP90/PSD-95-ASSOCIATED PROTEIN 2) (SAPAP2) (PSD-95/SAP90 BINDING PROTEIN 2) (FRAGMENT). [SWISSPROT;Acc:Q9P1A6] 0.411155456 no value
0.776201 2498 0.167149 "UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIAL PRECURSOR (EC 1.10.2.2). [SWISSPROT;Acc:P31930]" 0.215342418 UQCRC1
0.779209 642 0.209001 "TRANSCRIPTION FACTOR CP2; TRANSCRIPTION FACTOR CP2, ALPHA GLOBIN. [RefSeq;Acc:NM_005653]" 0.268222005 TFCP2
0.779889 452 0.215243 "PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 (EC 3.1.3.48) (PROTEIN-TYROSINE PHOSPHATASE 1B) (PTP-1B). [SWISSPROT;Acc:P18031]" 0.27599184 no value
0.77996 2984 0.107787 SPERMATOGENESIS ASSOCIATED 6. [RefSeq;Acc:NM_019073] 0.138195548 SPATA6
0.780167 1839 0.182207 40S RIBOSOMAL PROTEIN S24 (S19). [SWISSPROT;Acc:P16632] 0.233548715 RPS24
0.780188 270 0.239018 MAX PROTEIN. [SWISSPROT;Acc:P25912] 0.306359493 MAX
0.781248 3127 0.0574917 METALLOPROTEASE 1; METALLOPROTEASE 1 (PITRILYSIN FAMILY). [RefSeq;Acc:NM_014889] 0.073589564 PITRM1
0.782104 3093 0.0760798 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-5 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-5 SUBUNIT). [SWISSPROT;Acc:Q9UF02] 0.09727581 CACNG5

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/