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