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