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

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/