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