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.


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