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 Hugo final description Rank
Results: HTML CSV LaTeX Showing element 2158 to 2207 of 3206 in total
expected
measured
Hugo
final
description
Rank
0.882186 0.226073 CTPS2 0.256264552 CYTIDINE TRIPHOSPHATE SYNTHASE II; CTP SYNTHETASE TYPE 2; UTP-AMMONIA LIGASE; CTP SYNTHETASE ISOFORM; CYTIDINE 5'-TRIPHOSPHATE SYNTHETASE 2. [RefSeq;Acc:NM_019857] 959
0.882968 0.208499 GSTP1 0.236134265 GLUTATHIONE S-TRANSFERASE P (EC 2.5.1.18) (GST CLASS-PI) (GSTP1-1). [SWISSPROT;Acc:P09211] 1765
0.883788 0.210207 NLK 0.237847764 NEMO-LIKE KINASE; LIKELY ORTHOLOG OF MOUSE NEMO LIKE KINASE. [RefSeq;Acc:NM_016231] 1701
0.884993 0.192282 IMMP1L 0.217269515 2433
0.886465 0.255373 HMG20B 0.288080184 "HIGH-MOBILITY GROUP 20B; SOX-LIKE TRANSCRIPTIONAL FACTOR; SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY E, MEMBER 1-RELATED. [RefSeq;Acc:NM_006339]" 322
0.88694 0.226174 RRM2B 0.255004848 RIBONUCLEOTIDE REDUCTASE M2 B (TP53 INDUCIBLE); P53-INDUCIBLE RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT 2 HOMOLOG. [RefSeq;Acc:NM_015713] 997
0.887589 0.223627 GMPPB 0.251948819 GDP-MANNOSE PYROPHOSPHORYLASE B ISOFORM 1; MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE; AMPHOTERIN INDUCED GENE 3. [RefSeq;Acc:NM_013334] 1085
0.892542 0.225517 CLTCL1 0.252668222 CLATHRIN HEAVY CHAIN 2 (CLH-22). [SWISSPROT;Acc:P53675] 1059
0.892673 0.211834 ATP6V0A2 0.237303021 VACUOLAR PROTON TRANSLOCATING ATPASE 116 KDA SUBUNIT A ISOFORM 2 (V-ATPASE 116-KDA ISOFORM A2) (TJ6). [SWISSPROT;Acc:Q9Y487] 1718
0.894194 0.179735 TARSL2 0.201002243 2780
0.894645 0.217383 no value 0.242982412 TRANSCRIPTION FACTOR-LIKE PROTEIN MORF4 (MORTALITY FACTOR 4) (CELLULAR SENESCENCE-RELATED PROTEIN 1) (SEN1). [SWISSPROT;Acc:Q9Y690] 1472
0.894997 0.192216 ILK 0.2147672 INTEGRIN-LINKED PROTEIN KINASE 1 (EC 2.7.1.-) (ILK-1) (59 KDA SERINE/THREONINE PROTEIN KINASE) (P59ILK). [SWISSPROT;Acc:Q13418] 2512
0.897587 0.228495 TTRAP 0.254565853 TRAF AND TNF RECEPTOR-ASSOCIATED PROTEIN; ETS1-ASSOCIATED PROTEIN 2. [RefSeq;Acc:NM_016614] 1008
0.898593 0.194172 no value 0.216084479 2489
0.900943 0.238765 CAPZB 0.265016766 F-ACTIN CAPPING PROTEIN BETA SUBUNIT (CAPZ BETA). [SWISSPROT;Acc:P47756] 710
0.901215 0.214575 PPAT 0.238095238 AMIDOPHOSPHORIBOSYLTRANSFERASE PRECURSOR (EC 2.4.2.14) (GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE) (ATASE) (GPAT). [SWISSPROT;Acc:Q06203] 1687
0.90295 0.195152 FBLN2 0.216127139 FIBULIN-2 PRECURSOR. [SWISSPROT;Acc:P98095] 2488
0.904936 0.155306 UBE2G2 0.171620977 UBIQUITIN-CONJUGATING ENZYME E2 G2 (EC 6.3.2.19) (UBIQUITIN-PROTEIN LIGASE G2) (UBIQUITIN CARRIER PROTEIN G2). [SWISSPROT;Acc:P56554] 2917
0.905006 0.24526 CUGBP2 0.271003728 "CUG TRIPLET REPEAT, RNA BINDING PROTEIN 2; ELAV-TYPE RNA-BINDING PROTEIN; CUG TRIPLET REPEAT,RNA-BINDING PROTEIN 2; CUG TRIPLET REPEAT, RNA-BINDING PROTEIN 2; NEUROBLASTOMA APOPTOSIS-RELATED RNA-BINDING PROTEIN. [RefSeq;Acc:NM_006561]" 547
0.906259 0.233873 CCDC85A 0.258064196 910
0.906671 0.21933 no value 0.241906932 HISTONE H3.3 (H3.A) (H3.B) (H3.3Q). [SWISSPROT;Acc:P06351] 1539
0.907758 0.243481 UBP1 0.268222368 UPSTREAM BINDING PROTEIN 1 (LBP-1A). [RefSeq;Acc:NM_014517] 640
0.910326 0.222353 UBE2B 0.244256453 UBIQUITIN-CONJUGATING ENZYME E2 B (EC 6.3.2.19) (UBIQUITIN-PROTEIN LIGASE B) (UBIQUITIN CARRIER PROTEIN B) (HR6B) (HHR6B) (E2-17 KDA). [SWISSPROT;Acc:P23567] 1396
0.911432 0.218752 no value 0.240009128 TRANSLIN. [SWISSPROT;Acc:Q15631] 1600
0.912016 0.261495 VCP 0.286721943 TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATPASE) (15S MG(2+)- ATPASE P97 SUBUNIT) (VALOSIN CONTAINING PROTEIN) (VCP) [CONTAINS: VALOSIN]. [SWISSPROT;Acc:P55072] 325
0.912166 0.439158 NFYB 0.481445263 NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA (NF-Y PROTEIN CHAIN B) (NF-YB) (CCAAT-BINDING TRANSCRIPTION FACTOR SUBUNIT A) (CBF-A) (CAAT- BOX DNA BINDING PROTEIN SUBUNIT B). [SWISSPROT;Acc:P25208] 14
0.91233 0.2316 PRAM1 0.253855513 PRAM-1 PROTEIN; PML-RARA TARGET GENE ENCODING AN ADAPTOR MOLECULE-1. [RefSeq;Acc:NM_032152] 1016
0.914083 0.134987 CCNG1 0.147674774 CYCLIN G1 (CYCLIN G). [SWISSPROT;Acc:P51959] 2954
0.914445 0.250323 KIAA1217 0.27374309 510
0.916205 0.2305 PLEKHF2 0.251581251 PHAFIN 2; PH AND FYVE DOMAIN-CONTAINING PROTEIN 2. [RefSeq;Acc:NM_024613] 1090
0.916816 0.207889 no value 0.22675106 "GLYCINE CLEAVAGE SYSTEM H PROTEIN, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:P23434]" 2180
0.917867 0.214359 0.233540371 60S RIBOSOMAL PROTEIN L18A. [SWISSPROT;Acc:Q02543] 1844
0.920283 0.212972 CLP1 0.231420118 PRE-MRNA CLEAVAGE COMPLEX II PROTEIN CLP1. [SWISSPROT;Acc:Q92989] 1946
0.920789 0.378587 DLGAP1 0.411154999 DISKS LARGE-ASSOCIATED PROTEIN 1 (DAP-1) (GUANYLATE KINASE-ASSOCIATED PROTEIN) (HGKAP) (SAP90/PSD-95-ASSOCIATED PROTEIN 1) (SAPAP1) (PSD- 95/SAP90 BINDING PROTEIN 1). [SWISSPROT;Acc:O14490] 56
DLGAP4 DISKS LARGE-ASSOCIATED PROTEIN 4 (DAP-4) (SAP90/PSD-95-ASSOCIATED PROTEIN 4) (SAPAP4) (PSD-95/SAP90 BINDING PROTEIN 4). [SWISSPROT;Acc:Q9Y2H0] 57
0.920862 0.280486 HAT1 0.304590699 HISTONE ACETYLTRANSFERASE TYPE B CATALYTIC SUBUNIT (EC 2.3.1.48). [SWISSPROT;Acc:O14929] 277
0.924279 0.215775 SARS2 0.233452237 "SERYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRSMT). [SWISSPROT;Acc:Q9NP81]" 1847
0.925078 0.230865 AP1G1 0.24956274 ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT (GAMMA-ADAPTIN) (ADAPTOR PROTEIN COMPLEX AP-1 GAMMA-1 SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN GAMMA-1 SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 GAMMA-1 LARGE CHAIN). [SWISSPROT;Acc:O43747] 1162
0.927081 0.223546 BLOC1S1 0.241128877 GCN5-LIKE PROTEIN 1 (RT14 PROTEIN). [SWISSPROT;Acc:P78537] 1564
0.928542 0.251342 MAP2K1 0.270684579 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1 (EC 2.7.1.-) (MAP KINASE KINASE 1) (MAPKK 1) (ERK ACTIVATOR KINASE 1) (MAPK/ERK KINASE 1) (MEK1). [SWISSPROT;Acc:Q02750] 570
MAP2K2 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 2 (EC 2.7.1.-) (MAP KINASE KINASE 2) (MAPKK 2) (ERK ACTIVATOR KINASE 2) (MAPK/ERK KINASE 2) (MEK2). [SWISSPROT;Acc:P36507] 569
0.929064 0.24009 CCDC85B 0.258421379 DELTA-INTERACTING PROTEIN A (HEPATITIS DELTA ANTIGEN INTERACTING PROTEIN A). [SWISSPROT;Acc:Q15834] 906
0.929536 0.23379 CSNK2A1P 0.251512583 "CASEIN KINASE II, ALPHA CHAIN (CK II) (EC 2.7.1.37). [SWISSPROT;Acc:P19138]" 1094
CSNK2A2 "CASEIN KINASE II, ALPHA' CHAIN (CK II) (EC 2.7.1.37). [SWISSPROT;Acc:P19784]" 1093
0.930463 0.218499 PDCD5 0.234828252 PROGRAMMED CELL DEATH PROTEIN 5 (TFAR19 PROTEIN) (TF-1 CELL APOPTOSIS RELATED GENE-19 PROTEIN). [SWISSPROT;Acc:O14737] 1796
0.9315 0.163112 CCNB1 0.175106817 G2/MITOTIC-SPECIFIC CYCLIN B1. [SWISSPROT;Acc:P14635] 2896
0.932647 0.25098 ZIC3 0.269105031 ZINC FINGER PROTEIN ZIC 3 (ZINC FINGER PROTEIN OF THE CEREBELLUM 3). [SWISSPROT;Acc:O60481] 600
0.9333 0.25596 R3HDM2 0.274252652 497
0.933978 0.253813 PPP1R12A 0.271754795 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 12A; MYOSIN PHOSPHATASE, TARGET SUBUNIT 1. [RefSeq;Acc:NM_002480]" 529
0.939561 0.230116 DDX24 0.244918638 ATP-DEPENDENT RNA HELICASE DDX24 (DEAD-BOX PROTEIN 24). [SWISSPROT;Acc:Q9GZR7] 1363

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/