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

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/