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 description Hugo Rank final Gene measured
Results: HTML CSV LaTeX Showing element 2658 to 2707 of 3206 in total
expected
description
Hugo
Rank
final
measured
1.48829 RIBULOSE-5-PHOSPHATE-3-EPIMERASE; RIBULOSE 5-PHOSPHATE 3-EPIMERASE. [RefSeq;Acc:NM_006916] no value 2372 0.220049184 0.327497
1.48848 RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (RAF-1) (C-RAF). [SWISSPROT;Acc:P04049] RAF1 2955 0.147639202 0.219758
1.49161 SSU72 2755 0.203634998 0.303744
1.49174 MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A (MAD2-LIKE 1) (HSMAD2). [SWISSPROT;Acc:Q13257] MAD2L1 1190 0.248602303 0.37085
1.49189 "KARYOPHERIN BETA 2B, TRANSPORTIN; IMPORTIN 3. [RefSeq;Acc:NM_013433]" TNPO2 532 0.271387971 0.404881
1.49271 CAD PROTEIN [INCLUDES: GLUTAMINE-DEPENDENT CARBAMOYL-PHOSPHATE SYNTHASE (EC 6.3.5.5); ASPARTATE CARBAMOYLTRANSFERASE (EC 2.1.3.2); DIHYDROOROTASE (EC 3.5.2.3)]. [SWISSPROT;Acc:P27708] CAD 2083 0.229024392 0.341867
1.49288 40S RIBOSOMAL PROTEIN S13. [SWISSPROT;Acc:Q02546] RPS13 1897 0.232570602 0.3472
1.49712 HEPATOCYTE NUCLEAR FACTOR 3-ALPHA (HNF-3A) (FORKHEAD BOX PROTEIN A1). [SWISSPROT;Acc:P55317] FOXA1 580 0.270110612 0.404388
1.5 XPA BINDING PROTEIN 1; MBD2 INTERACTOR PROTEIN; PUTATIVE ATP(GTP)-BINDING PROTEIN. [RefSeq;Acc:NM_007266] XAB1 11 0.542592 0.813888
1.50518 TRANSCRIPTION INITIATION FACTOR TFIID 100 KDA SUBUNIT (TAFII-100) (TAFII100). [SWISSPROT;Acc:Q15542] TAF5 2368 0.220147756 0.331362
1.50657 C-TERMINAL BINDING PROTEIN 2 (CTBP2). [SWISSPROT;Acc:P56545] CTBP2 738 0.264639545 0.398698
1.50787 CYSTEINE ENDOPEPTIDASE AUT-LIKE 2 ISOFORM A; AUTOPHAGY-RELATED CYSTEINE ENDOPEPTIDASE 2; AUTOPHAGIN 2. [RefSeq;Acc:NM_052936] ATG4A 3067 0.103512902 0.156084
1.50997 TYROSINE-PROTEIN KINASE FRK (EC 2.7.1.112) (NUCLEAR TYROSINE PROTEIN KINASE RAK). [SWISSPROT;Acc:P42685] FRK 27 0.426117737 0.643425
1.51127 "VACUOLAR ATP SYNTHASE SUBUNIT B, BRAIN ISOFORM (EC 3.6.3.14) (V-ATPASE B2 SUBUNIT) (VACUOLAR PROTON PUMP B ISOFORM 2) (ENDOMEMBRANE PROTON PUMP 58 KDA SUBUNIT) (HO57). [SWISSPROT;Acc:P21281]" ATP6V1B2 1744 0.236717463 0.357744
1.51635 AUTOPHAGY PROTEIN 5-LIKE (APG5-LIKE) (APOPTOSIS-SPECIFIC PROTEIN). [SWISSPROT;Acc:Q9H1Y0] ATG5 653 0.267820754 0.40611
1.5203 FARNESYL PYROPHOSPHATE SYNTHETASE (FPP SYNTHETASE) (FPS) (FARNESYL DIPHOSPHATE SYNTHETASE) [INCLUDES: DIMETHYLALLYLTRANSFERASE (EC 2.5.1.1); GERANYLTRANSTRANSFERASE (EC 2.5.1.10)]. [SWISSPROT;Acc:P14324] FDPS 2365 0.220296652 0.334917
1.52156 ARP2/3 COMPLEX 16 KDA SUBUNIT (P16-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 5). [SWISSPROT;Acc:O15511] ARPC5 717 0.264795999 0.402903
1.52661 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1 (EC 5.2.1.8) (ROTAMASE PIN1) (PPIASE PIN1). [SWISSPROT;Acc:Q13526] PIN1 2139 0.22782374 0.347798
1.52927 TRANSFORMING PROTEIN P21/H-RAS-1 (C-H-RAS). [SWISSPROT;Acc:P01112] HRAS 2961 0.146163856 0.223524
1.5325 BIFUNCTIONAL AMINOACYL-TRNA SYNTHETASE [INCLUDES: GLUTAMYL-TRNA SYNTHETASE (EC 6.1.1.17) (GLUTAMATE--TRNA LIGASE); PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE)]. [SWISSPROT;Acc:P07814] EPRS 2353 0.220368026 0.337714
1.53626 "PYRUVATE DEHYDROGENASE E1 COMPONENT ALPHA SUBUNIT, TESTIS-SPECIFIC FORM, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-A TYPE II). [SWISSPROT;Acc:P29803]" PDHA2 2030 0.230296304 0.353795
1.53719 "ADENYLATE KINASE ISOENZYME 4, MITOCHONDRIAL (EC 2.7.4.3) (ATP-AMP TRANSPHOSPHORYLASE). [SWISSPROT;Acc:P27144]" no value 1967 0.231217351 0.355425
1.53743 HEPATOCYTE NUCLEAR FACTOR 3-BETA (HNF-3B) (FORKHEAD BOX PROTEIN A2). [SWISSPROT;Acc:Q9Y261] FOXA2 596 0.269294862 0.414022
1.54054 CLATHRIN COAT ASSEMBLY PROTEIN AP50 (CLATHRIN COAT ASSOCIATED PROTEIN AP50) (PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN) (HA2 50 KDA SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 MEDIUM CHAIN) (AP-2 MU 2 CHAIN). [SWISSPROT;Acc:P20172] AP2M1 2912 0.174141535 0.268272
1.54946 "PROBABLE DIMETHYLADENOSINE TRANSFERASE (EC 2.1.1.-) (S- ADENOSYLMETHIONINE-6-N',N'-ADENOSYL(RRNA) DIMETHYLTRANSFERASE) (18S RRNA DIMETHYLASE). [SWISSPROT;Acc:Q9UNQ2]" DIMT1L 1722 0.237161334 0.367472
1.55176 PUTATIVE SIALOGLYCOPROTEASE TYPE 2. [RefSeq;Acc:NM_022353] OSGEPL1 1783 0.235285096 0.365106
1.55221 "EGF-LIKE-DOMAIN, MULTIPLE 7; NEU1 PROTEIN. [RefSeq;Acc:NM_016215]" EGFL7 3124 0.075688857 0.117485
1.55638 60S RIBOSOMAL PROTEIN L18. [SWISSPROT;Acc:Q07020] RPL18 2132 0.227977743 0.35482
1.55794 RNA-BINDING PROTEIN 9 (RNA BINDING MOTIF PROTEIN 9) (HEXARIBONUCLEOTIDE BINDING PROTEIN 2) (REPRESSOR OF TAMOXIFEN TRANSCRIPTIONAL ACTIVITY). [SWISSPROT;Acc:O43251] RBM9 514 0.27250536 0.424547
1.55897 DIPHTHAMIDE BIOSYNTHESIS-LIKE PROTEIN 2. [RefSeq;Acc:NM_001384] DPH2 2278 0.222553994 0.346955
1.56247 C9orf41 125 0.357121097 0.557991
1.56343 CYTOPLASMIC PROTEIN NCK2 (NCK ADAPTOR PROTEIN 2) (SH2/SH3 ADAPTOR PROTEIN NCK-BETA) (NCK-2). [SWISSPROT;Acc:O43639] NCK2 268 0.307242409 0.480352
1.56403 EUKARYOTIC TRANSLATION INITIATION FACTOR 5A (EIF-5A) (EIF-4D) (REV- BINDING FACTOR). [SWISSPROT;Acc:P10159] EIF5AP1 1586 0.24075817 0.376553
1.57686 WD-REPEAT PROTEIN 3. [SWISSPROT;Acc:Q9UNX4] WDR3 1454 0.243150311 0.383414
1.57699 GERM CELL-LESS. [RefSeq;Acc:NM_022471] no value 1060 0.25263762 0.398407
1.57827 DYNACTIN COMPLEX 50 KDA SUBUNIT (50 KDA DYNEIN-ASSOCIATED POLYPEPTIDE) (DYNAMITIN) (DCTN-50) (DYNACTIN 2). [SWISSPROT;Acc:Q13561] DCTN2 1694 0.237869946 0.375423
1.57878 "BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.42) (BCAT(M)) (PLACENTAL PROTEIN 18) (PP18). [SWISSPROT;Acc:O15382]" BCAT2 1452 0.243340427 0.384181
1.58875 NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA (NF-Y PROTEIN CHAIN C) (NUCLEAR FACTOR YC) (NF-YC) (CCAAT-BINDING TRANSCRIPTION FACTOR SUBUNIT C) (CBF-C) (TRANSACTIVATOR HSM-1/2). [SWISSPROT;Acc:Q13952] NFYC 3115 0.090676318 0.144062
1.59051 HEMK PROTEIN HOMOLOG (EC 2.1.1.-) (M.HSAHEMKP). [SWISSPROT;Acc:Q9Y5R4] HEMK1 2484 0.216265852 0.343973
1.59398 CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 4. [RefSeq;Acc:NM_030627] CPEB4 3071 0.103197029 0.164494
1.59695 NUCLEOSIDE DIPHOSPHATE KINASE 3 (EC 2.7.4.6) (NDK 3) (NDP KINASE 3) (NM23-H3) (DR-NM23). [SWISSPROT;Acc:Q13232] NME3 2065 0.229464291 0.366443
1.59883 APG3P; PC3-96 PROTEIN. [RefSeq;Acc:NM_022488] ATG3 3000 0.128961803 0.206188
1.59982 XPA-BINDING PROTEIN 2 (HCNP PROTEIN) (PP3898). [SWISSPROT;Acc:Q9HCS7] XAB2 451 0.27604418 0.441621
1.60336 KH-TYPE SPLICING REGULATORY PROTEIN (FUSE BINDING PROTEIN 2); KH-TYPE SPLICING REGULATORY PROTEIN (FUSE-BINDING PROTEIN 2). [RefSeq;Acc:NM_003685] KHSRP 833 0.260980067 0.418445
1.60341 HELICASE (FRAGMENT). [SPTREMBL;Acc:Q92771] no value 2767 0.202098029 0.324046
1.60405 ARPC5L 719 0.264769178 0.424703
1.60594 CDC42-INTERACTING PROTEIN 4 (THYROID RECEPTOR INTERACTING PROTEIN 10) (TRIP-10). [SWISSPROT;Acc:Q15642] TRIP10 384 0.279042804 0.448126
1.60666 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM2 (SMALL NUCLEAR RIBONUCLEAR PROTEIN D HOMOLOG) (G7B) (SNRNP CORE SM-LIKE PROTEIN SM-X5). [SWISSPROT;Acc:Q9Y333] no value 1487 0.242827979 0.390142
1.60733 CDA11 PROTEIN. [RefSeq;Acc:NM_032026] TATDN1 1777 0.235579501 0.378654
1.61155 GUANYLATE KINASE (EC 2.7.4.8) (GMP KINASE). [SWISSPROT;Acc:Q16774] GUK1 2392 0.219554466 0.353823

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/