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 measured Rank Hugo description final
Results: HTML CSV LaTeX Showing element 302 to 351 of 3206 in total
expected
measured
Rank
Hugo
description
final
0.132688 0.0345092 881 PIK3C2A "PHOSPHOINOSITIDE-3-KINASE, CLASS 2, ALPHA POLYPEPTIDE; C2-CONTAINING PHOSPHATIDYLINOSITOL KINASE. [RefSeq;Acc:NM_002645]" 0.260077776
0.132771 0.0359807 559 TBC1D22B TBC1 DOMAIN FAMILY PROTEIN C22ORF4-LIKE (FRAGMENT). [SWISSPROT;Acc:Q9NU19] 0.270998185
0.132897 0.0370257 396 TSR2 0.278604483
0.133236 0.0315727 1741 COTL1 COACTOSIN-LIKE PROTEIN. [SWISSPROT;Acc:Q14019] 0.236968237
0.133476 0.0297305 2268 LTA4H LEUKOTRIENE A-4 HYDROLASE (EC 3.3.2.6) (LTA-4 HYDROLASE) (LEUKOTRIENE A(4) HYDROLASE). [SWISSPROT;Acc:P09960] 0.222740418
0.133763 0.0362497 555 C20orf118 DJ132F21.2 (CONTAINS A NOVEL PROTEIN SIMILAR TO THE L82E FROM DROSOPHILA) (FRAGMENT). [SPTREMBL;Acc:Q9H125] 0.270999454
0.133775 0.0295892 2336 C1orf50 0.22118632
0.134108 0.035822 660 SMOC2 SECRETED MODULAR CALCIUM-BINDING PROTEIN 2; SMOOTH MUSCLE ASSOCIATED PROTEIN 2. [RefSeq;Acc:NM_022138] 0.267113073
0.13446 0.0307532 2089 ARHGEF9 CDC42 GUANINE EXCHANGE FACTOR 9; HPEM-2 COLLYBISTIN. [RefSeq;Acc:NM_015185] 0.228716347
0.134819 0.031449 1863 DOLK 0.233268308
0.134909 0.0355674 767 RAB11FIP2 0.263639935
0.135208 0.0348108 931 SCOC SHORT COILED-COIL PROTEIN; SHORT COILED COIL PROTEIN. [RefSeq;Acc:NM_032547] 0.257461097
0.135226 0.0331688 1336 CREBL1 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-6 BETA (ACTIVATING TRANSCRIPTION FACTOR 6 BETA) (ATF6-BETA) (CAMP RESPONSIVE ELEMENT BINDING PROTEIN-LIKE 1) (CAMP RESPONSE ELEMENT BINDING PROTEIN-RELATED PROTEIN) (CREB-RP) (G13 PROTEIN). [SWISSPROT;A 0.245284191
0.135465 0.0349547 912 SLC37A2 0.258034917
0.135522 0.0333011 1314 P4HA1 "PROLYL 4-HYDROXYLASE ALPHA-1 SUBUNIT PRECURSOR (EC 1.14.11.2) (4-PH ALPHA-1) (PROCOLLAGEN-PROLINE,2-OXOGLUTARATE-4-DIOXYGENASE ALPHA-1 SUBUNIT). [SWISSPROT;Acc:P13674]" 0.245724679
0.135679 0.0359748 708 RCOR3 0.265146412
0.135713 0.0319409 1779 RDH8 RETINOL DEHYDROGENASE 8 (ALL-TRANS); PHOTORECEPTOR OUTER SEGMENT ALL-TRANS RETINOL DEHYDROGENASE. [RefSeq;Acc:NM_015725] 0.23535623
0.135722 0.0340698 1104 SNRPB2 "U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B"". [SWISSPROT;Acc:P08579]" 0.251026363
0.135742 0.0374708 450 ISY1 0.27604426
0.135904 0.027794 2743 GCLC GLUTAMATE--CYSTEINE LIGASE CATALYTIC SUBUNIT (EC 6.3.2.2) (GAMMA- GLUTAMYLCYSTEINE SYNTHETASE) (GAMMA-ECS) (GCS HEAVY CHAIN). [SWISSPROT;Acc:P48506] 0.204512008
0.135906 0.0342868 1072 CSE1L IMPORTIN-ALPHA RE-EXPORTER (CHROMOSOME SEGREGATION 1-LIKE PROTEIN) (CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN). [SWISSPROT;Acc:P55060] 0.252283196
0.136094 0.0368814 554 no value SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN 2 (FOVEA-ASSOCIATED SH3 DOMAIN BINDING PROTEIN). [SWISSPROT;Acc:Q9UJC5] 0.270999456
0.1362 0.0330661 1499 IPO8 IMPORTIN 8; RAN-BINDING PROTEIN 8. [RefSeq;Acc:NM_006390] 0.242776065
0.136218 0.0344183 1054 PDCL PHOSDUCIN-LIKE PROTEIN (PHLP). [SWISSPROT;Acc:Q13371] 0.252670719
1055 RAD52 DNA REPAIR PROTEIN RAD52 HOMOLOG. [SWISSPROT;Acc:P43351]
0.136317 0.0315866 1930 CWF19L2 0.231714313
0.136588 0.0335632 1306 HABP4 HYALURONAN BINDING PROTEIN 4; INTRACELLULAR ANTIGEN DETECTED BY MONOCLONAL ANTIBODY KI-1; INTRACELLULAR HYALURONAN-BINDING PROTEIN; CHROMODOMAIN HELICASE DNA BINDING PROTEIN 3 INTERACTING PROTEIN. [RefSeq;Acc:NM_014282] 0.245725832
0.136653 0.0298377 2415 SERINC3 TUMOR DIFFERENTIALLY EXPRESSED PROTEIN 1 (TRANSMEMBRANE PROTEIN SBBI99). [SWISSPROT;Acc:Q13530] 0.218346469
2416 MAF1 HOMOLOG OF YEAST MAF1. [RefSeq;Acc:NM_032272]
0.136657 0.0360283 763 RAB11FIP1 RAB COUPLING PROTEIN; RAB-INTERACTING RECYCLING PROTEIN; RAB EFFECTOR PROTEIN; RAB11-FAMILY INTERACTING PROTEIN 1. [RefSeq;Acc:NM_025151] 0.263640355
0.136688 0.032514 1692 SLC25A5 "ADP,ATP CARRIER PROTEIN, FIBROBLAST ISOFORM (ADP/ATP TRANSLOCASE 2) (ADENINE NUCLEOTIDE TRANSLOCATOR 2) (ANT 2). [SWISSPROT;Acc:P05141]" 0.237870186
1693 SLC25A4 "ADP,ATP CARRIER PROTEIN, HEART/SKELETAL MUSCLE ISOFORM T1 (ADP/ATP TRANSLOCASE 1) (ADENINE NUCLEOTIDE TRANSLOCATOR 1) (ANT 1). [SWISSPROT;Acc:P12235]"
0.136931 0.0370824 564 GALNTL1 SIMILAR TO EXPRESSED SEQUENCE AI415388 (FRAGMENT). [SPTREMBL;Acc:Q8N428] 0.270810846
0.136958 0.0349473 987 ABT1 ACTIVATOR OF BASAL TRANSCRIPTION 1; TATA-BINDING PROTEIN-BINDING PROTEIN; BASAL TRANSCRIPTIONAL ACTIVATOR. [RefSeq;Acc:NM_013375] 0.255168008
0.13696 0.031325 2088 no value 0.228716414
0.137154 0.0326245 1697 ASNS ASPARAGINE SYNTHETASE [GLUTAMINE-HYDROLYZING] (EC 6.3.5.4) (GLUTAMINE- DEPENDENT ASPARAGINE SYNTHETASE) (TS11 CELL CYCLE CONTROL PROTEIN). [SWISSPROT;Acc:P08243] 0.237867652
0.137173 0.0371738 556 SH3BGRL SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN. [SWISSPROT;Acc:O75368] 0.270999395
0.137326 0.0315458 2056 COQ10A 0.229714694
0.137332 0.0339667 1259 AQR 0.247332741
0.137792 0.0377969 482 SLC23A2 "SOLUTE CARRIER FAMILY 23, MEMBER 2 (SODIUM-DEPENDENT VITAMIN C TRANSPORTER 2) (HSVCT2) (NA(+)/L-ASCORBIC ACID TRANSPORTER 2) (YOLK SAC PERMEASE-LIKE MOLECULE 2) (NUCLEOBASE TRANSPORTER-LIKE 1 PROTEIN). [SWISSPROT;Acc:Q9UGH3]" 0.274304023
0.138013 0.0325717 1767 TRIP12 THYROID RECEPTOR INTERACTING PROTEIN 12 (TRIP12). [SWISSPROT;Acc:Q14669] 0.236004579
0.138116 0.0378858 476 SHC3 NEURONAL SHC. [RefSeq;Acc:NM_016848] 0.274304208
0.138197 0.0379081 475 SHC2 PROTEIN SCK (FRAGMENT). [SWISSPROT;Acc:P98077] 0.274304797
0.138505 0.0349396 1078 UBE2W 0.252262373
0.138512 0.0308958 2261 ATPAF1 0.223055042
0.0384193 418 C8orf79 0.277371636
0.138615 0.0309189 2254 C7orf24 0.223055946
0.138666 0.0416551 299 KLF5 KRUEPPEL-LIKE FACTOR 5 (INTESTINAL-ENRICHED KRUEPPEL-LIKE FACTOR) (COLON KRUEPPEL-LIKE FACTOR) (TRANSCRIPTION FACTOR BTEB2) (BASIC TRANSCRIPTION ELEMENT BINDING PROTEIN 2) (BTE-BINDING PROTEIN 2) (GC BOX BINDING PROTEIN 2). [SWISSPROT;Acc:Q13887] 0.3003988
0.138711 0.0365698 766 C14orf122 PROTEIN C14ORF122 (CGI-112). [SWISSPROT;Acc:Q9Y3B6] 0.26364023
0.138821 0.0376313 541 LRRC4 NAG14 PROTEIN. [RefSeq;Acc:NM_022143] 0.271077863

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/