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