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 Rank measured Gene Hugo description final
Results: HTML CSV LaTeX Showing element 2652 to 2701 of 3206 in total
expected
Rank
measured
Hugo
description
final
1.48057 1397 0.361623 EIF2S3 EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 3 (EUKARYOTIC TRANSLATION INITIATION FACTOR 2 GAMMA SUBUNIT) (EIF-2-GAMMA). [SWISSPROT;Acc:P41091] 0.244245797
1.48145 2956 0.218717 ARAF A-RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (A-RAF-1) (PROTO-ONCOGENE PKS). [SWISSPROT;Acc:P10398] 0.147637112
1.48248 2467 0.321097 RNASEH2A RIBONUCLEASE HI LARGE SUBUNIT (EC 3.1.26.-) (RNASE HI LARGE SUBUNIT) (RNASE H(35)) (RIBONUCLEASE H2) (RNASE H2). [SWISSPROT;Acc:O75792] 0.21659449
1.48326 839 0.386694 LAMC1 LAMININ GAMMA-1 CHAIN PRECURSOR (LAMININ B2 CHAIN). [SWISSPROT;Acc:P11047] 0.260705473
1.48471 725 0.392968 ARPC3 ARP2/3 COMPLEX 21 KDA SUBUNIT (P21-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 3). [SWISSPROT;Acc:O15145] 0.264676604
1.48707 2962 0.217355 no value TRANSFORMING PROTEIN N-RAS. [SWISSPROT;Acc:P01111] 0.146163261
1.48829 2372 0.327497 RIBULOSE-5-PHOSPHATE-3-EPIMERASE; RIBULOSE 5-PHOSPHATE 3-EPIMERASE. [RefSeq;Acc:NM_006916] 0.220049184
1.48848 2955 0.219758 RAF1 RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (RAF-1) (C-RAF). [SWISSPROT;Acc:P04049] 0.147639202
1.49161 2755 0.303744 SSU72 0.203634998
1.49174 1190 0.37085 MAD2L1 MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A (MAD2-LIKE 1) (HSMAD2). [SWISSPROT;Acc:Q13257] 0.248602303
1.49189 532 0.404881 TNPO2 "KARYOPHERIN BETA 2B, TRANSPORTIN; IMPORTIN 3. [RefSeq;Acc:NM_013433]" 0.271387971
1.49271 2083 0.341867 CAD 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] 0.229024392
1.49288 1897 0.3472 RPS13 40S RIBOSOMAL PROTEIN S13. [SWISSPROT;Acc:Q02546] 0.232570602
1.49712 580 0.404388 FOXA1 HEPATOCYTE NUCLEAR FACTOR 3-ALPHA (HNF-3A) (FORKHEAD BOX PROTEIN A1). [SWISSPROT;Acc:P55317] 0.270110612
1.5 11 0.813888 XAB1 XPA BINDING PROTEIN 1; MBD2 INTERACTOR PROTEIN; PUTATIVE ATP(GTP)-BINDING PROTEIN. [RefSeq;Acc:NM_007266] 0.542592
1.50518 2368 0.331362 TAF5 TRANSCRIPTION INITIATION FACTOR TFIID 100 KDA SUBUNIT (TAFII-100) (TAFII100). [SWISSPROT;Acc:Q15542] 0.220147756
1.50657 738 0.398698 CTBP2 C-TERMINAL BINDING PROTEIN 2 (CTBP2). [SWISSPROT;Acc:P56545] 0.264639545
1.50787 3067 0.156084 ATG4A CYSTEINE ENDOPEPTIDASE AUT-LIKE 2 ISOFORM A; AUTOPHAGY-RELATED CYSTEINE ENDOPEPTIDASE 2; AUTOPHAGIN 2. [RefSeq;Acc:NM_052936] 0.103512902
1.50997 27 0.643425 FRK TYROSINE-PROTEIN KINASE FRK (EC 2.7.1.112) (NUCLEAR TYROSINE PROTEIN KINASE RAK). [SWISSPROT;Acc:P42685] 0.426117737
1.51127 1744 0.357744 ATP6V1B2 "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]" 0.236717463
1.51635 653 0.40611 ATG5 AUTOPHAGY PROTEIN 5-LIKE (APG5-LIKE) (APOPTOSIS-SPECIFIC PROTEIN). [SWISSPROT;Acc:Q9H1Y0] 0.267820754
1.5203 2365 0.334917 FDPS 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] 0.220296652
1.52156 717 0.402903 ARPC5 ARP2/3 COMPLEX 16 KDA SUBUNIT (P16-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 5). [SWISSPROT;Acc:O15511] 0.264795999
1.52661 2139 0.347798 PIN1 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1 (EC 5.2.1.8) (ROTAMASE PIN1) (PPIASE PIN1). [SWISSPROT;Acc:Q13526] 0.22782374
1.52927 2961 0.223524 HRAS TRANSFORMING PROTEIN P21/H-RAS-1 (C-H-RAS). [SWISSPROT;Acc:P01112] 0.146163856
1.5325 2353 0.337714 EPRS 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] 0.220368026
1.53626 2030 0.353795 PDHA2 "PYRUVATE DEHYDROGENASE E1 COMPONENT ALPHA SUBUNIT, TESTIS-SPECIFIC FORM, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-A TYPE II). [SWISSPROT;Acc:P29803]" 0.230296304
1.53719 1967 0.355425 no value "ADENYLATE KINASE ISOENZYME 4, MITOCHONDRIAL (EC 2.7.4.3) (ATP-AMP TRANSPHOSPHORYLASE). [SWISSPROT;Acc:P27144]" 0.231217351
1.53743 596 0.414022 FOXA2 HEPATOCYTE NUCLEAR FACTOR 3-BETA (HNF-3B) (FORKHEAD BOX PROTEIN A2). [SWISSPROT;Acc:Q9Y261] 0.269294862
1.54054 2912 0.268272 AP2M1 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] 0.174141535
1.54946 1722 0.367472 DIMT1L "PROBABLE DIMETHYLADENOSINE TRANSFERASE (EC 2.1.1.-) (S- ADENOSYLMETHIONINE-6-N',N'-ADENOSYL(RRNA) DIMETHYLTRANSFERASE) (18S RRNA DIMETHYLASE). [SWISSPROT;Acc:Q9UNQ2]" 0.237161334
1.55176 1783 0.365106 OSGEPL1 PUTATIVE SIALOGLYCOPROTEASE TYPE 2. [RefSeq;Acc:NM_022353] 0.235285096
1.55221 3124 0.117485 EGFL7 "EGF-LIKE-DOMAIN, MULTIPLE 7; NEU1 PROTEIN. [RefSeq;Acc:NM_016215]" 0.075688857
1.55638 2132 0.35482 RPL18 60S RIBOSOMAL PROTEIN L18. [SWISSPROT;Acc:Q07020] 0.227977743
1.55794 514 0.424547 RBM9 RNA-BINDING PROTEIN 9 (RNA BINDING MOTIF PROTEIN 9) (HEXARIBONUCLEOTIDE BINDING PROTEIN 2) (REPRESSOR OF TAMOXIFEN TRANSCRIPTIONAL ACTIVITY). [SWISSPROT;Acc:O43251] 0.27250536
1.55897 2278 0.346955 DPH2 DIPHTHAMIDE BIOSYNTHESIS-LIKE PROTEIN 2. [RefSeq;Acc:NM_001384] 0.222553994
1.56247 125 0.557991 C9orf41 0.357121097
1.56343 268 0.480352 NCK2 CYTOPLASMIC PROTEIN NCK2 (NCK ADAPTOR PROTEIN 2) (SH2/SH3 ADAPTOR PROTEIN NCK-BETA) (NCK-2). [SWISSPROT;Acc:O43639] 0.307242409
1.56403 1586 0.376553 EIF5AP1 EUKARYOTIC TRANSLATION INITIATION FACTOR 5A (EIF-5A) (EIF-4D) (REV- BINDING FACTOR). [SWISSPROT;Acc:P10159] 0.24075817
1.57686 1454 0.383414 WDR3 WD-REPEAT PROTEIN 3. [SWISSPROT;Acc:Q9UNX4] 0.243150311
1.57699 1060 0.398407 no value GERM CELL-LESS. [RefSeq;Acc:NM_022471] 0.25263762
1.57827 1694 0.375423 DCTN2 DYNACTIN COMPLEX 50 KDA SUBUNIT (50 KDA DYNEIN-ASSOCIATED POLYPEPTIDE) (DYNAMITIN) (DCTN-50) (DYNACTIN 2). [SWISSPROT;Acc:Q13561] 0.237869946
1.57878 1452 0.384181 BCAT2 "BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.42) (BCAT(M)) (PLACENTAL PROTEIN 18) (PP18). [SWISSPROT;Acc:O15382]" 0.243340427
1.58875 3115 0.144062 NFYC 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] 0.090676318
1.59051 2484 0.343973 HEMK1 HEMK PROTEIN HOMOLOG (EC 2.1.1.-) (M.HSAHEMKP). [SWISSPROT;Acc:Q9Y5R4] 0.216265852
1.59398 3071 0.164494 CPEB4 CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 4. [RefSeq;Acc:NM_030627] 0.103197029
1.59695 2065 0.366443 NME3 NUCLEOSIDE DIPHOSPHATE KINASE 3 (EC 2.7.4.6) (NDK 3) (NDP KINASE 3) (NM23-H3) (DR-NM23). [SWISSPROT;Acc:Q13232] 0.229464291
1.59883 3000 0.206188 ATG3 APG3P; PC3-96 PROTEIN. [RefSeq;Acc:NM_022488] 0.128961803
1.59982 451 0.441621 XAB2 XPA-BINDING PROTEIN 2 (HCNP PROTEIN) (PP3898). [SWISSPROT;Acc:Q9HCS7] 0.27604418
1.60336 833 0.418445 KHSRP KH-TYPE SPLICING REGULATORY PROTEIN (FUSE BINDING PROTEIN 2); KH-TYPE SPLICING REGULATORY PROTEIN (FUSE-BINDING PROTEIN 2). [RefSeq;Acc:NM_003685] 0.260980067

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/