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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measured Rank Gene Hugo description final expected
Results: HTML CSV LaTeX Showing element 3158 to 3206 of 3206 in total
measured
Rank
Hugo
description
final
expected
1.19046 1614 PSMC6 26S PROTEASE REGULATORY SUBUNIT S10B (PROTEASOME SUBUNIT P42) (P44) (CONSERVED ATPASE DOMAIN PROTEIN 44) (CADP44). [SWISSPROT;Acc:Q92524] 0.239730317 4.96583
1.20591 86 GIPC1 RGS19-INTERACTING PROTEIN 1 (GAIP C-TERMINUS INTERACTING PROTEIN GIPC) (RGS-GAIP INTERACTING PROTEIN) (TAX INTERACTION PROTEIN 2) (TIP-2). [SWISSPROT;Acc:O14908] 0.385693725 3.1266
1.23017 1980 MRPL36 "60S RIBOSOMAL PROTEIN L36, MITOCHONDRIAL PRECURSOR (L36MT) (BRCA1- INTERACTING PROTEIN 1). [SWISSPROT;Acc:Q9P0J6]" 0.231010465 5.32517
1.2328 1936 CDH1 EPITHELIAL-CADHERIN PRECURSOR (E-CADHERIN) (UVOMORULIN) (CADHERIN-1) (CAM 120/80). [SWISSPROT;Acc:P12830] 0.231690563 5.32089
1.24311 954 KPNA1 IMPORTIN ALPHA-1 SUBUNIT (KARYOPHERIN ALPHA-1 SUBUNIT) (SRP1-BETA) (RAG COHORT PROTEIN 2) (NUCLEOPROTEIN INTERACTOR 1) (NPI-1). [SWISSPROT;Acc:P52294] 0.256363141 4.84902
1.24769 1935 no value C367G8.3 (NOVEL PROTEIN SIMILAR TO RPL23A (60S RIBOSOMAL PROTEIN L23A)) (60S RIBOSOMAL PROTEIN L23A LIKE). [SPTREMBL;Acc:Q9BR02] 0.231690854 5.38515
1.26742 1644 PSMD4 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 (26S PROTEASOME REGULATORY SUBUNIT S5A) (RPN10) (MULTIUBIQUITIN CHAIN BINDING PROTEIN) (ANTISECRETORY FACTOR-1) (AF) (ASF). [SWISSPROT;Acc:P55036] 0.239024455 5.30247
1.27676 2016 no value PUTATIVE EUKARYOTIC TRANSLATION INITIATION FACTOR 1A (EIF-1A) (EIF- 4C). [SWISSPROT;Acc:O75642] 0.230592791 5.53686
1.27878 1247 FBL FIBRILLARIN (34 KDA NUCLEOLAR SCLERODERMA ANTIGEN). [SWISSPROT;Acc:P22087] 0.247558353 5.16557
1.28125 2 RINT1 RAD50-INTERACTING PROTEIN 1. [RefSeq;Acc:NM_021930] 1.097524413 1.1674
3 RHOBTB2 RHO-RELATED BTB DOMAIN-CONTAINING PROTEIN 2 (DELETED IN BREAST CANCER 2 GENE PROTEIN) (P83). [SWISSPROT;Acc:Q9BYZ6]
1.29605 1942 RPL35 60S RIBOSOMAL PROTEIN L35. [SWISSPROT;Acc:P42766] 0.231604586 5.59596
1.29995 155 HOXD9 HOMEOBOX PROTEIN HOX-D9 (HOX-4C) (HOX-5.2). [SWISSPROT;Acc:P28356] 0.351139491 3.70209
1.30722 1957 SEC61A2 PROTEIN TRANSPORT PROTEIN SEC61 ALPHA SUBUNIT ISOFORM 2 (SEC61 ALPHA- 2). [SWISSPROT;Acc:Q9Y2R3] 0.23125586 5.6527
1.32337 1945 RPL26 60S RIBOSOMAL PROTEIN L26. [SWISSPROT;Acc:Q02877] 0.231568504 5.71481
1.32362 1943 no value 40S RIBOSOMAL PROTEIN S15 (RIG PROTEIN). [SWISSPROT;Acc:P11174] 0.231599281 5.71513
1.3237 1944 MRPL2 MITOCHONDRIAL RIBOSOMAL PROTEIN L2. [RefSeq;Acc:NM_015950] 0.231598285 5.7155
1.32564 1954 SEC61A1 PROTEIN TRANSPORT PROTEIN SEC61 ALPHA SUBUNIT ISOFORM 1 (SEC61 ALPHA- 1). [SWISSPROT;Acc:P38378] 0.231256346 5.73234
1.33288 696 MAPK1 MITOGEN-ACTIVATED PROTEIN KINASE 1 (EC 2.7.1.37) (EXTRACELLULAR SIGNAL-REGULATED KINASE 2) (ERK-2) (MITOGEN-ACTIVATED PROTEIN KINASE 2) (MAP KINASE 2) (MAPK 2) (P42-MAPK) (ERT1). [SWISSPROT;Acc:P28482] 0.265639356 5.01763
1.34083 1893 RPL3L 60S RIBOSOMAL PROTEIN L3-LIKE. [SWISSPROT;Acc:Q92901] 0.232687649 5.76236
1.36156 1909 MRPL3 MITOCHONDRIAL 60S RIBOSOMAL PROTEIN L3 (L3MT). [SWISSPROT;Acc:P09001] 0.232177358 5.86431
1.37404 937 KPNA6 IMPORTIN ALPHA-6 SUBUNIT (KARYOPHERIN ALPHA-5 SUBUNIT). [SWISSPROT;Acc:O15131] 0.256444999 5.35803
1.38784 1430 PSMA1 PROTEASOME SUBUNIT ALPHA TYPE 1 (EC 3.4.25.1) (PROTEASOME COMPONENT C2) (MACROPAIN SUBUNIT C2) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C2) (PROTEASOME NU CHAIN) (30 KDA PROSOMAL PROTEIN) (PROS-30). [SWISSPROT;Acc:P25786] 0.243783507 5.69292
1.40328 1934 no value 60S RIBOSOMAL PROTEIN L23A. [SWISSPROT;Acc:P29316] 0.231696263 6.05655
1.41778 1968 RPL5 60S RIBOSOMAL PROTEIN L5. [SWISSPROT;Acc:P46777] 0.231174608 6.13294
1.42729 67 PEX5 PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR (PEROXISMORE RECEPTOR 1) (PEROXISOMAL C-TERMINAL TARGETING SIGNAL IMPORT RECEPTOR) (PTS1-BP) (PEROXIN-5) (PTS1 RECEPTOR). [SWISSPROT;Acc:P50542] 0.406127379 3.51439
1.4649 23 GRAP GRB2-RELATED ADAPTOR PROTEIN. [SWISSPROT;Acc:Q13588] 0.47451533 3.08715
1.469 2012 no value 40S RIBOSOMAL PROTEIN S2 (S4) (LLREP3 PROTEIN). [SWISSPROT;Acc:P15880] 0.230625641 6.36963
1.48249 209 PAH PHENYLALANINE-4-HYDROXYLASE (EC 1.14.16.1) (PAH) (PHE-4- MONOOXYGENASE). [SWISSPROT;Acc:P00439] 0.320555013 4.62476
1.5119 352 ACTN4 ALPHA-ACTININ 4 (NON-MUSCLE ALPHA-ACTININ 4) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:O43707] 0.282415485 5.35346
1.51643 1908 RPS3 40S RIBOSOMAL PROTEIN S3. [SWISSPROT;Acc:P23396] 0.232182447 6.5312
1.53732 351 ACTN1 ALPHA-ACTININ 1 (ALPHA-ACTININ CYTOSKELETAL ISOFORM) (NON-MUSCLE ALPHA-ACTININ 1) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:P12814] 0.282429972 5.44319
1.5466 1339 GTPBP2 GTP BINDING PROTEIN 2. [RefSeq;Acc:NM_019096] 0.245282989 6.30537
1.55851 2046 POLR1C DNA-DIRECTED RNA POLYMERASE I 40 KDA POLYPEPTIDE (EC 2.7.7.6) (RPA40) (RPA39). [SWISSPROT;Acc:O15160] 0.230004088 6.77601
1.60424 2070 POLR2C DNA-DIRECTED RNA POLYMERASE II 33 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB3) (RNA POLYMERASE II SUBUNIT 3) (RPB33) (RPB31). [SWISSPROT;Acc:P19387] 0.229451173 6.99164
1.64337 3139 NSMCE4A 0.065381739 25.135
1.66627 43 WASL NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN (N-WASP). [SWISSPROT;Acc:O00401] 0.420351716 3.96399
1.69676 437 EYA2 EYES ABSENT HOMOLOG 2. [SWISSPROT;Acc:O00167] 0.277166394 6.12181
1.73296 404 USO1 GENERAL VESICULAR TRANSPORT FACTOR P115 (TRANSCYTOSIS ASSOCIATED PROTEIN) (TAP) (VESICLE DOCKING PROTEIN). [SWISSPROT;Acc:O60763] 0.278252157 6.22802
1.76022 436 EYA1 EYES ABSENT HOMOLOG 1. [SWISSPROT;Acc:Q99502] 0.2771677 6.35074
1.76157 435 EYA4 EYES ABSENT HOMOLOG 4. [SWISSPROT;Acc:O95677] 0.277255851 6.35359
1.799 345 ACTN2 ALPHA-ACTININ 2 (ALPHA ACTININ SKELETAL MUSCLE ISOFORM 2) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:P35609] 0.282555533 6.36689
1.83106 466 PDLIM5 LIM PROTEIN (SIMILAR TO RAT PROTEIN KINASE C-BINDING ENIGMA); ENIGMA HOMOLOG. [RefSeq;Acc:NM_006457] 0.275552894 6.64504
1.95189 15 GRB2 GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2 (GRB2 ADAPTER PROTEIN) (SH2/SH3 ADAPTER GRB2) (ASH PROTEIN). [SWISSPROT;Acc:P29354] 0.475589342 4.10415
1.97356 31 WAS WISKOTT-ALDRICH SYNDROME PROTEIN (WASP). [SWISSPROT;Acc:P42768] 0.421390214 4.68345
2.06651 410 EYA3 EYES ABSENT HOMOLOG 3. [SWISSPROT;Acc:Q99504] 0.27779854 7.43888
2.17256 291 KLHL8 KELCH-LIKE PROTEIN 8. [SWISSPROT;Acc:Q9P2G9] 0.301808998 7.19846
2.49065 458 LDB3 ZASP PROTEIN (FRAGMENT). [SPTREMBL;Acc:Q9Y4Z3] 0.275601573 9.03714
3.66001 4 no value 1.097520091 3.3348

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/