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

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/