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

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/