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 measured Hugo description final
Results: HTML CSV LaTeX Showing element 2152 to 2201 of 3206 in total
expected
Rank
measured
Hugo
description
final
0.879442 904 0.227308 PPIL4 PEPTIDYLPROLYL ISOMERASE-LIKE 4; CYCLOPHILIN-TYPE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE; PPIASE; SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-18. [RefSeq;Acc:NM_139126] 0.258468438
0.880269 1627 0.210706 PRKACB "CAMP-DEPENDENT PROTEIN KINASE, BETA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-BETA). [SWISSPROT;Acc:P22694]" 0.239365467
1628 PRKACA "CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-ALPHA). [SWISSPROT;Acc:P17612]"
0.88087 383 0.245859 PEX19 PEROXISOMAL FARNESYLATED PROTEIN (33 KDA HOUSEKEEPING PROTEIN) (PEROXIN 19). [SWISSPROT;Acc:P40855] 0.27910929
0.88153 605 0.237139 OTX1 HOMEOBOX PROTEIN OTX1. [SWISSPROT;Acc:P32242] 0.269008429
0.88182 3022 0.106813 SEPT10 SEPTIN 10 ISOFORM 1. [RefSeq;Acc:NM_144710] 0.121127895
0.882186 959 0.226073 CTPS2 CYTIDINE TRIPHOSPHATE SYNTHASE II; CTP SYNTHETASE TYPE 2; UTP-AMMONIA LIGASE; CTP SYNTHETASE ISOFORM; CYTIDINE 5'-TRIPHOSPHATE SYNTHETASE 2. [RefSeq;Acc:NM_019857] 0.256264552
0.882968 1765 0.208499 GSTP1 GLUTATHIONE S-TRANSFERASE P (EC 2.5.1.18) (GST CLASS-PI) (GSTP1-1). [SWISSPROT;Acc:P09211] 0.236134265
0.883788 1701 0.210207 NLK NEMO-LIKE KINASE; LIKELY ORTHOLOG OF MOUSE NEMO LIKE KINASE. [RefSeq;Acc:NM_016231] 0.237847764
0.884993 2433 0.192282 IMMP1L 0.217269515
0.886465 322 0.255373 HMG20B "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]" 0.288080184
0.88694 997 0.226174 RRM2B RIBONUCLEOTIDE REDUCTASE M2 B (TP53 INDUCIBLE); P53-INDUCIBLE RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT 2 HOMOLOG. [RefSeq;Acc:NM_015713] 0.255004848
0.887589 1085 0.223627 GMPPB GDP-MANNOSE PYROPHOSPHORYLASE B ISOFORM 1; MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE; AMPHOTERIN INDUCED GENE 3. [RefSeq;Acc:NM_013334] 0.251948819
0.892542 1059 0.225517 CLTCL1 CLATHRIN HEAVY CHAIN 2 (CLH-22). [SWISSPROT;Acc:P53675] 0.252668222
0.892673 1718 0.211834 ATP6V0A2 VACUOLAR PROTON TRANSLOCATING ATPASE 116 KDA SUBUNIT A ISOFORM 2 (V-ATPASE 116-KDA ISOFORM A2) (TJ6). [SWISSPROT;Acc:Q9Y487] 0.237303021
0.894194 2780 0.179735 TARSL2 0.201002243
0.894645 1472 0.217383 no value TRANSCRIPTION FACTOR-LIKE PROTEIN MORF4 (MORTALITY FACTOR 4) (CELLULAR SENESCENCE-RELATED PROTEIN 1) (SEN1). [SWISSPROT;Acc:Q9Y690] 0.242982412
0.894997 2512 0.192216 ILK INTEGRIN-LINKED PROTEIN KINASE 1 (EC 2.7.1.-) (ILK-1) (59 KDA SERINE/THREONINE PROTEIN KINASE) (P59ILK). [SWISSPROT;Acc:Q13418] 0.2147672
0.897587 1008 0.228495 TTRAP TRAF AND TNF RECEPTOR-ASSOCIATED PROTEIN; ETS1-ASSOCIATED PROTEIN 2. [RefSeq;Acc:NM_016614] 0.254565853
0.898593 2489 0.194172 no value 0.216084479
0.900943 710 0.238765 CAPZB F-ACTIN CAPPING PROTEIN BETA SUBUNIT (CAPZ BETA). [SWISSPROT;Acc:P47756] 0.265016766
0.901215 1687 0.214575 PPAT AMIDOPHOSPHORIBOSYLTRANSFERASE PRECURSOR (EC 2.4.2.14) (GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE) (ATASE) (GPAT). [SWISSPROT;Acc:Q06203] 0.238095238
0.90295 2488 0.195152 FBLN2 FIBULIN-2 PRECURSOR. [SWISSPROT;Acc:P98095] 0.216127139
0.904936 2917 0.155306 UBE2G2 UBIQUITIN-CONJUGATING ENZYME E2 G2 (EC 6.3.2.19) (UBIQUITIN-PROTEIN LIGASE G2) (UBIQUITIN CARRIER PROTEIN G2). [SWISSPROT;Acc:P56554] 0.171620977
0.905006 547 0.24526 CUGBP2 "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]" 0.271003728
0.906259 910 0.233873 CCDC85A 0.258064196
0.906671 1539 0.21933 no value HISTONE H3.3 (H3.A) (H3.B) (H3.3Q). [SWISSPROT;Acc:P06351] 0.241906932
0.907758 640 0.243481 UBP1 UPSTREAM BINDING PROTEIN 1 (LBP-1A). [RefSeq;Acc:NM_014517] 0.268222368
0.910326 1396 0.222353 UBE2B 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] 0.244256453
0.911432 1600 0.218752 no value TRANSLIN. [SWISSPROT;Acc:Q15631] 0.240009128
0.912016 325 0.261495 VCP TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATPASE) (15S MG(2+)- ATPASE P97 SUBUNIT) (VALOSIN CONTAINING PROTEIN) (VCP) [CONTAINS: VALOSIN]. [SWISSPROT;Acc:P55072] 0.286721943
0.912166 14 0.439158 NFYB 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] 0.481445263
0.91233 1016 0.2316 PRAM1 PRAM-1 PROTEIN; PML-RARA TARGET GENE ENCODING AN ADAPTOR MOLECULE-1. [RefSeq;Acc:NM_032152] 0.253855513
0.914083 2954 0.134987 CCNG1 CYCLIN G1 (CYCLIN G). [SWISSPROT;Acc:P51959] 0.147674774
0.914445 510 0.250323 KIAA1217 0.27374309
0.916205 1090 0.2305 PLEKHF2 PHAFIN 2; PH AND FYVE DOMAIN-CONTAINING PROTEIN 2. [RefSeq;Acc:NM_024613] 0.251581251
0.916816 2180 0.207889 no value "GLYCINE CLEAVAGE SYSTEM H PROTEIN, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:P23434]" 0.22675106
0.917867 1844 0.214359 60S RIBOSOMAL PROTEIN L18A. [SWISSPROT;Acc:Q02543] 0.233540371
0.920283 1946 0.212972 CLP1 PRE-MRNA CLEAVAGE COMPLEX II PROTEIN CLP1. [SWISSPROT;Acc:Q92989] 0.231420118
0.920789 56 0.378587 DLGAP1 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] 0.411154999
57 DLGAP4 DISKS LARGE-ASSOCIATED PROTEIN 4 (DAP-4) (SAP90/PSD-95-ASSOCIATED PROTEIN 4) (SAPAP4) (PSD-95/SAP90 BINDING PROTEIN 4). [SWISSPROT;Acc:Q9Y2H0]
0.920862 277 0.280486 HAT1 HISTONE ACETYLTRANSFERASE TYPE B CATALYTIC SUBUNIT (EC 2.3.1.48). [SWISSPROT;Acc:O14929] 0.304590699
0.924279 1847 0.215775 SARS2 "SERYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRSMT). [SWISSPROT;Acc:Q9NP81]" 0.233452237
0.925078 1162 0.230865 AP1G1 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] 0.24956274
0.927081 1564 0.223546 BLOC1S1 GCN5-LIKE PROTEIN 1 (RT14 PROTEIN). [SWISSPROT;Acc:P78537] 0.241128877
0.928542 569 0.251342 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] 0.270684579
570 MAP2K1 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]
0.929064 906 0.24009 CCDC85B DELTA-INTERACTING PROTEIN A (HEPATITIS DELTA ANTIGEN INTERACTING PROTEIN A). [SWISSPROT;Acc:Q15834] 0.258421379
0.929536 1093 0.23379 CSNK2A2 "CASEIN KINASE II, ALPHA' CHAIN (CK II) (EC 2.7.1.37). [SWISSPROT;Acc:P19784]" 0.251512583
1094 CSNK2A1P "CASEIN KINASE II, ALPHA CHAIN (CK II) (EC 2.7.1.37). [SWISSPROT;Acc:P19138]"

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/