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