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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Gene expected Rank Hugo description measured final
Results: HTML CSV LaTeX Showing element 3158 to 3206 of 3206 in total
expected
Rank
Hugo
description
measured
final
4.7257 2036 RPS5 40S RIBOSOMAL PROTEIN S5. [SWISSPROT;Acc:P46782] 1.08774 0.230175424
4.73611 1958 MRPL12 "60S RIBOSOMAL PROTEIN L12, MITOCHONDRIAL PRECURSOR (L12MT) (5C5-2). [SWISSPROT;Acc:P52815]" 1.09511 0.231225626
4.76096 1389 PSMD14 26S PROTEASOME-ASSOCIATED PAD1 HOMOLOG. [RefSeq;Acc:NM_005805] 1.1639 0.244467502
4.7857 2502 no value KERATIN ASSOCIATED PROTEIN 9-4; KERATIN ASSOCIATED PROTEIN 9.4. [RefSeq;Acc:NM_033191] 1.02862 0.214936164
4.84902 954 KPNA1 IMPORTIN ALPHA-1 SUBUNIT (KARYOPHERIN ALPHA-1 SUBUNIT) (SRP1-BETA) (RAG COHORT PROTEIN 2) (NUCLEOPROTEIN INTERACTOR 1) (NPI-1). [SWISSPROT;Acc:P52294] 1.24311 0.256363141
4.8561 1526 UTP20 DOWN-REGULATED IN METASTASIS. [RefSeq;Acc:NM_014503] 1.17672 0.242317909
4.96583 1614 PSMC6 26S PROTEASE REGULATORY SUBUNIT S10B (PROTEASOME SUBUNIT P42) (P44) (CONSERVED ATPASE DOMAIN PROTEIN 44) (CADP44). [SWISSPROT;Acc:Q92524] 1.19046 0.239730317
5.01763 696 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] 1.33288 0.265639356
5.14358 1978 MRPL17 MITOCHONDRIAL RIBOSOMAL PROTEIN L17; LYST-INTERACTING PROTEIN LIP2. [RefSeq;Acc:NM_022061] 1.18829 0.231023917
5.16557 1247 FBL FIBRILLARIN (34 KDA NUCLEOLAR SCLERODERMA ANTIGEN). [SWISSPROT;Acc:P22087] 1.27878 0.247558353
5.2164 2548 KRTAP9-8 KERATIN ASSOCIATED PROTEIN 9.2. [RefSeq;Acc:NM_031961] 1.11949 0.214609693
5.26987 2757 ACACA ACETYL-COA CARBOXYLASE 1 (EC 6.4.1.2) (ACC-ALPHA) [INCLUDES: BIOTIN CARBOXYLASE (EC 6.3.4.14)]. [SWISSPROT;Acc:Q13085] 1.06806 0.202672931
5.29857 2537 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]" 1.13737 0.21465603
5.30247 1644 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] 1.26742 0.239024455
5.32089 1936 CDH1 EPITHELIAL-CADHERIN PRECURSOR (E-CADHERIN) (UVOMORULIN) (CADHERIN-1) (CAM 120/80). [SWISSPROT;Acc:P12830] 1.2328 0.231690563
5.32517 1980 MRPL36 "60S RIBOSOMAL PROTEIN L36, MITOCHONDRIAL PRECURSOR (L36MT) (BRCA1- INTERACTING PROTEIN 1). [SWISSPROT;Acc:Q9P0J6]" 1.23017 0.231010465
5.35346 352 ACTN4 ALPHA-ACTININ 4 (NON-MUSCLE ALPHA-ACTININ 4) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:O43707] 1.5119 0.282415485
5.35803 937 KPNA6 IMPORTIN ALPHA-6 SUBUNIT (KARYOPHERIN ALPHA-5 SUBUNIT). [SWISSPROT;Acc:O15131] 1.37404 0.256444999
5.38515 1935 no value C367G8.3 (NOVEL PROTEIN SIMILAR TO RPL23A (60S RIBOSOMAL PROTEIN L23A)) (60S RIBOSOMAL PROTEIN L23A LIKE). [SPTREMBL;Acc:Q9BR02] 1.24769 0.231690854
5.44319 351 ACTN1 ALPHA-ACTININ 1 (ALPHA-ACTININ CYTOSKELETAL ISOFORM) (NON-MUSCLE ALPHA-ACTININ 1) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:P12814] 1.53732 0.282429972
5.53686 2016 no value PUTATIVE EUKARYOTIC TRANSLATION INITIATION FACTOR 1A (EIF-1A) (EIF- 4C). [SWISSPROT;Acc:O75642] 1.27676 0.230592791
5.59596 1942 RPL35 60S RIBOSOMAL PROTEIN L35. [SWISSPROT;Acc:P42766] 1.29605 0.231604586
5.6527 1957 SEC61A2 PROTEIN TRANSPORT PROTEIN SEC61 ALPHA SUBUNIT ISOFORM 2 (SEC61 ALPHA- 2). [SWISSPROT;Acc:Q9Y2R3] 1.30722 0.23125586
5.69292 1430 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] 1.38784 0.243783507
5.71481 1945 RPL26 60S RIBOSOMAL PROTEIN L26. [SWISSPROT;Acc:Q02877] 1.32337 0.231568504
5.71513 1943 no value 40S RIBOSOMAL PROTEIN S15 (RIG PROTEIN). [SWISSPROT;Acc:P11174] 1.32362 0.231599281
5.7155 1944 MRPL2 MITOCHONDRIAL RIBOSOMAL PROTEIN L2. [RefSeq;Acc:NM_015950] 1.3237 0.231598285
5.73234 1954 SEC61A1 PROTEIN TRANSPORT PROTEIN SEC61 ALPHA SUBUNIT ISOFORM 1 (SEC61 ALPHA- 1). [SWISSPROT;Acc:P38378] 1.32564 0.231256346
5.76236 1893 RPL3L 60S RIBOSOMAL PROTEIN L3-LIKE. [SWISSPROT;Acc:Q92901] 1.34083 0.232687649
5.86431 1909 MRPL3 MITOCHONDRIAL 60S RIBOSOMAL PROTEIN L3 (L3MT). [SWISSPROT;Acc:P09001] 1.36156 0.232177358
6.01339 3088 DYNLT1 CYTOPLASMIC DYNEIN LIGHT CHAIN (T-COMPLEX TESTIS-SPECIFIC PROTEIN 1 HOMOLOG) (PROTEIN CW-1). [SWISSPROT;Acc:Q15763] 0.587123 0.097635942
6.05655 1934 no value 60S RIBOSOMAL PROTEIN L23A. [SWISSPROT;Acc:P29316] 1.40328 0.231696263
6.12181 437 EYA2 EYES ABSENT HOMOLOG 2. [SWISSPROT;Acc:O00167] 1.69676 0.277166394
6.13294 1968 RPL5 60S RIBOSOMAL PROTEIN L5. [SWISSPROT;Acc:P46777] 1.41778 0.231174608
6.22802 404 USO1 GENERAL VESICULAR TRANSPORT FACTOR P115 (TRANSCYTOSIS ASSOCIATED PROTEIN) (TAP) (VESICLE DOCKING PROTEIN). [SWISSPROT;Acc:O60763] 1.73296 0.278252157
6.30537 1339 GTPBP2 GTP BINDING PROTEIN 2. [RefSeq;Acc:NM_019096] 1.5466 0.245282989
6.35074 436 EYA1 EYES ABSENT HOMOLOG 1. [SWISSPROT;Acc:Q99502] 1.76022 0.2771677
6.35359 435 EYA4 EYES ABSENT HOMOLOG 4. [SWISSPROT;Acc:O95677] 1.76157 0.277255851
6.36689 345 ACTN2 ALPHA-ACTININ 2 (ALPHA ACTININ SKELETAL MUSCLE ISOFORM 2) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:P35609] 1.799 0.282555533
6.36963 2012 no value 40S RIBOSOMAL PROTEIN S2 (S4) (LLREP3 PROTEIN). [SWISSPROT;Acc:P15880] 1.469 0.230625641
6.5312 1908 RPS3 40S RIBOSOMAL PROTEIN S3. [SWISSPROT;Acc:P23396] 1.51643 0.232182447
6.64504 466 PDLIM5 LIM PROTEIN (SIMILAR TO RAT PROTEIN KINASE C-BINDING ENIGMA); ENIGMA HOMOLOG. [RefSeq;Acc:NM_006457] 1.83106 0.275552894
6.77601 2046 POLR1C DNA-DIRECTED RNA POLYMERASE I 40 KDA POLYPEPTIDE (EC 2.7.7.6) (RPA40) (RPA39). [SWISSPROT;Acc:O15160] 1.55851 0.230004088
6.99164 2070 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] 1.60424 0.229451173
7.19846 291 KLHL8 KELCH-LIKE PROTEIN 8. [SWISSPROT;Acc:Q9P2G9] 2.17256 0.301808998
7.43888 410 EYA3 EYES ABSENT HOMOLOG 3. [SWISSPROT;Acc:Q99504] 2.06651 0.27779854
9.03714 458 LDB3 ZASP PROTEIN (FRAGMENT). [SPTREMBL;Acc:Q9Y4Z3] 2.49065 0.275601573
11.3823 3167 C5orf33 0.73655 0.06471012
25.135 3139 NSMCE4A 1.64337 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/