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