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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expected measured Hugo Gene description Rank final
Results: HTML CSV LaTeX Showing element 3158 to 3206 of 3206 in total
expected
measured
Hugo
description
Rank
final
4.7257 1.08774 RPS5 40S RIBOSOMAL PROTEIN S5. [SWISSPROT;Acc:P46782] 2036 0.230175424
4.73611 1.09511 MRPL12 "60S RIBOSOMAL PROTEIN L12, MITOCHONDRIAL PRECURSOR (L12MT) (5C5-2). [SWISSPROT;Acc:P52815]" 1958 0.231225626
4.76096 1.1639 PSMD14 26S PROTEASOME-ASSOCIATED PAD1 HOMOLOG. [RefSeq;Acc:NM_005805] 1389 0.244467502
4.7857 1.02862 no value KERATIN ASSOCIATED PROTEIN 9-4; KERATIN ASSOCIATED PROTEIN 9.4. [RefSeq;Acc:NM_033191] 2502 0.214936164
4.84902 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] 954 0.256363141
4.8561 1.17672 UTP20 DOWN-REGULATED IN METASTASIS. [RefSeq;Acc:NM_014503] 1526 0.242317909
4.96583 1.19046 PSMC6 26S PROTEASE REGULATORY SUBUNIT S10B (PROTEASOME SUBUNIT P42) (P44) (CONSERVED ATPASE DOMAIN PROTEIN 44) (CADP44). [SWISSPROT;Acc:Q92524] 1614 0.239730317
5.01763 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] 696 0.265639356
5.14358 1.18829 MRPL17 MITOCHONDRIAL RIBOSOMAL PROTEIN L17; LYST-INTERACTING PROTEIN LIP2. [RefSeq;Acc:NM_022061] 1978 0.231023917
5.16557 1.27878 FBL FIBRILLARIN (34 KDA NUCLEOLAR SCLERODERMA ANTIGEN). [SWISSPROT;Acc:P22087] 1247 0.247558353
5.2164 1.11949 KRTAP9-8 KERATIN ASSOCIATED PROTEIN 9.2. [RefSeq;Acc:NM_031961] 2548 0.214609693
5.26987 1.06806 ACACA ACETYL-COA CARBOXYLASE 1 (EC 6.4.1.2) (ACC-ALPHA) [INCLUDES: BIOTIN CARBOXYLASE (EC 6.3.4.14)]. [SWISSPROT;Acc:Q13085] 2757 0.202672931
5.29857 1.13737 BCKDK "[3-METHYL-2-OXOBUTANOATE DEHYDROGENASE [LIPOAMIDE]] KINASE, MITOCHONDRIAL PRECURSOR (EC 2.7.1.115) (BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE KINASE) (BCKDHKIN) (BCKD-KINASE). [SWISSPROT;Acc:O14874]" 2537 0.21465603
5.30247 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] 1644 0.239024455
5.32089 1.2328 CDH1 EPITHELIAL-CADHERIN PRECURSOR (E-CADHERIN) (UVOMORULIN) (CADHERIN-1) (CAM 120/80). [SWISSPROT;Acc:P12830] 1936 0.231690563
5.32517 1.23017 MRPL36 "60S RIBOSOMAL PROTEIN L36, MITOCHONDRIAL PRECURSOR (L36MT) (BRCA1- INTERACTING PROTEIN 1). [SWISSPROT;Acc:Q9P0J6]" 1980 0.231010465
5.35346 1.5119 ACTN4 ALPHA-ACTININ 4 (NON-MUSCLE ALPHA-ACTININ 4) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:O43707] 352 0.282415485
5.35803 1.37404 KPNA6 IMPORTIN ALPHA-6 SUBUNIT (KARYOPHERIN ALPHA-5 SUBUNIT). [SWISSPROT;Acc:O15131] 937 0.256444999
5.38515 1.24769 no value C367G8.3 (NOVEL PROTEIN SIMILAR TO RPL23A (60S RIBOSOMAL PROTEIN L23A)) (60S RIBOSOMAL PROTEIN L23A LIKE). [SPTREMBL;Acc:Q9BR02] 1935 0.231690854
5.44319 1.53732 ACTN1 ALPHA-ACTININ 1 (ALPHA-ACTININ CYTOSKELETAL ISOFORM) (NON-MUSCLE ALPHA-ACTININ 1) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:P12814] 351 0.282429972
5.53686 1.27676 no value PUTATIVE EUKARYOTIC TRANSLATION INITIATION FACTOR 1A (EIF-1A) (EIF- 4C). [SWISSPROT;Acc:O75642] 2016 0.230592791
5.59596 1.29605 RPL35 60S RIBOSOMAL PROTEIN L35. [SWISSPROT;Acc:P42766] 1942 0.231604586
5.6527 1.30722 SEC61A2 PROTEIN TRANSPORT PROTEIN SEC61 ALPHA SUBUNIT ISOFORM 2 (SEC61 ALPHA- 2). [SWISSPROT;Acc:Q9Y2R3] 1957 0.23125586
5.69292 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] 1430 0.243783507
5.71481 1.32337 RPL26 60S RIBOSOMAL PROTEIN L26. [SWISSPROT;Acc:Q02877] 1945 0.231568504
5.71513 1.32362 no value 40S RIBOSOMAL PROTEIN S15 (RIG PROTEIN). [SWISSPROT;Acc:P11174] 1943 0.231599281
5.7155 1.3237 MRPL2 MITOCHONDRIAL RIBOSOMAL PROTEIN L2. [RefSeq;Acc:NM_015950] 1944 0.231598285
5.73234 1.32564 SEC61A1 PROTEIN TRANSPORT PROTEIN SEC61 ALPHA SUBUNIT ISOFORM 1 (SEC61 ALPHA- 1). [SWISSPROT;Acc:P38378] 1954 0.231256346
5.76236 1.34083 RPL3L 60S RIBOSOMAL PROTEIN L3-LIKE. [SWISSPROT;Acc:Q92901] 1893 0.232687649
5.86431 1.36156 MRPL3 MITOCHONDRIAL 60S RIBOSOMAL PROTEIN L3 (L3MT). [SWISSPROT;Acc:P09001] 1909 0.232177358
6.01339 0.587123 DYNLT1 CYTOPLASMIC DYNEIN LIGHT CHAIN (T-COMPLEX TESTIS-SPECIFIC PROTEIN 1 HOMOLOG) (PROTEIN CW-1). [SWISSPROT;Acc:Q15763] 3088 0.097635942
6.05655 1.40328 no value 60S RIBOSOMAL PROTEIN L23A. [SWISSPROT;Acc:P29316] 1934 0.231696263
6.12181 1.69676 EYA2 EYES ABSENT HOMOLOG 2. [SWISSPROT;Acc:O00167] 437 0.277166394
6.13294 1.41778 RPL5 60S RIBOSOMAL PROTEIN L5. [SWISSPROT;Acc:P46777] 1968 0.231174608
6.22802 1.73296 USO1 GENERAL VESICULAR TRANSPORT FACTOR P115 (TRANSCYTOSIS ASSOCIATED PROTEIN) (TAP) (VESICLE DOCKING PROTEIN). [SWISSPROT;Acc:O60763] 404 0.278252157
6.30537 1.5466 GTPBP2 GTP BINDING PROTEIN 2. [RefSeq;Acc:NM_019096] 1339 0.245282989
6.35074 1.76022 EYA1 EYES ABSENT HOMOLOG 1. [SWISSPROT;Acc:Q99502] 436 0.2771677
6.35359 1.76157 EYA4 EYES ABSENT HOMOLOG 4. [SWISSPROT;Acc:O95677] 435 0.277255851
6.36689 1.799 ACTN2 ALPHA-ACTININ 2 (ALPHA ACTININ SKELETAL MUSCLE ISOFORM 2) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:P35609] 345 0.282555533
6.36963 1.469 no value 40S RIBOSOMAL PROTEIN S2 (S4) (LLREP3 PROTEIN). [SWISSPROT;Acc:P15880] 2012 0.230625641
6.5312 1.51643 RPS3 40S RIBOSOMAL PROTEIN S3. [SWISSPROT;Acc:P23396] 1908 0.232182447
6.64504 1.83106 PDLIM5 LIM PROTEIN (SIMILAR TO RAT PROTEIN KINASE C-BINDING ENIGMA); ENIGMA HOMOLOG. [RefSeq;Acc:NM_006457] 466 0.275552894
6.77601 1.55851 POLR1C DNA-DIRECTED RNA POLYMERASE I 40 KDA POLYPEPTIDE (EC 2.7.7.6) (RPA40) (RPA39). [SWISSPROT;Acc:O15160] 2046 0.230004088
6.99164 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] 2070 0.229451173
7.19846 2.17256 KLHL8 KELCH-LIKE PROTEIN 8. [SWISSPROT;Acc:Q9P2G9] 291 0.301808998
7.43888 2.06651 EYA3 EYES ABSENT HOMOLOG 3. [SWISSPROT;Acc:Q99504] 410 0.27779854
9.03714 2.49065 LDB3 ZASP PROTEIN (FRAGMENT). [SPTREMBL;Acc:Q9Y4Z3] 458 0.275601573
11.3823 0.73655 C5orf33 3167 0.06471012
25.135 1.64337 NSMCE4A 3139 0.065381739

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/