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 measured description Hugo final
Results: HTML CSV LaTeX Showing element 3158 to 3206 of 3206 in total
expected
Rank
measured
description
Hugo
final
4.7257 2036 1.08774 40S RIBOSOMAL PROTEIN S5. [SWISSPROT;Acc:P46782] RPS5 0.230175424
4.73611 1958 1.09511 "60S RIBOSOMAL PROTEIN L12, MITOCHONDRIAL PRECURSOR (L12MT) (5C5-2). [SWISSPROT;Acc:P52815]" MRPL12 0.231225626
4.76096 1389 1.1639 26S PROTEASOME-ASSOCIATED PAD1 HOMOLOG. [RefSeq;Acc:NM_005805] PSMD14 0.244467502
4.7857 2502 1.02862 KERATIN ASSOCIATED PROTEIN 9-4; KERATIN ASSOCIATED PROTEIN 9.4. [RefSeq;Acc:NM_033191] no value 0.214936164
4.84902 954 1.24311 IMPORTIN ALPHA-1 SUBUNIT (KARYOPHERIN ALPHA-1 SUBUNIT) (SRP1-BETA) (RAG COHORT PROTEIN 2) (NUCLEOPROTEIN INTERACTOR 1) (NPI-1). [SWISSPROT;Acc:P52294] KPNA1 0.256363141
4.8561 1526 1.17672 DOWN-REGULATED IN METASTASIS. [RefSeq;Acc:NM_014503] UTP20 0.242317909
4.96583 1614 1.19046 26S PROTEASE REGULATORY SUBUNIT S10B (PROTEASOME SUBUNIT P42) (P44) (CONSERVED ATPASE DOMAIN PROTEIN 44) (CADP44). [SWISSPROT;Acc:Q92524] PSMC6 0.239730317
5.01763 696 1.33288 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] MAPK1 0.265639356
5.14358 1978 1.18829 MITOCHONDRIAL RIBOSOMAL PROTEIN L17; LYST-INTERACTING PROTEIN LIP2. [RefSeq;Acc:NM_022061] MRPL17 0.231023917
5.16557 1247 1.27878 FIBRILLARIN (34 KDA NUCLEOLAR SCLERODERMA ANTIGEN). [SWISSPROT;Acc:P22087] FBL 0.247558353
5.2164 2548 1.11949 KERATIN ASSOCIATED PROTEIN 9.2. [RefSeq;Acc:NM_031961] KRTAP9-8 0.214609693
5.26987 2757 1.06806 ACETYL-COA CARBOXYLASE 1 (EC 6.4.1.2) (ACC-ALPHA) [INCLUDES: BIOTIN CARBOXYLASE (EC 6.3.4.14)]. [SWISSPROT;Acc:Q13085] ACACA 0.202672931
5.29857 2537 1.13737 "[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]" BCKDK 0.21465603
5.30247 1644 1.26742 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] PSMD4 0.239024455
5.32089 1936 1.2328 EPITHELIAL-CADHERIN PRECURSOR (E-CADHERIN) (UVOMORULIN) (CADHERIN-1) (CAM 120/80). [SWISSPROT;Acc:P12830] CDH1 0.231690563
5.32517 1980 1.23017 "60S RIBOSOMAL PROTEIN L36, MITOCHONDRIAL PRECURSOR (L36MT) (BRCA1- INTERACTING PROTEIN 1). [SWISSPROT;Acc:Q9P0J6]" MRPL36 0.231010465
5.35346 352 1.5119 ALPHA-ACTININ 4 (NON-MUSCLE ALPHA-ACTININ 4) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:O43707] ACTN4 0.282415485
5.35803 937 1.37404 IMPORTIN ALPHA-6 SUBUNIT (KARYOPHERIN ALPHA-5 SUBUNIT). [SWISSPROT;Acc:O15131] KPNA6 0.256444999
5.38515 1935 1.24769 C367G8.3 (NOVEL PROTEIN SIMILAR TO RPL23A (60S RIBOSOMAL PROTEIN L23A)) (60S RIBOSOMAL PROTEIN L23A LIKE). [SPTREMBL;Acc:Q9BR02] no value 0.231690854
5.44319 351 1.53732 ALPHA-ACTININ 1 (ALPHA-ACTININ CYTOSKELETAL ISOFORM) (NON-MUSCLE ALPHA-ACTININ 1) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:P12814] ACTN1 0.282429972
5.53686 2016 1.27676 PUTATIVE EUKARYOTIC TRANSLATION INITIATION FACTOR 1A (EIF-1A) (EIF- 4C). [SWISSPROT;Acc:O75642] no value 0.230592791
5.59596 1942 1.29605 60S RIBOSOMAL PROTEIN L35. [SWISSPROT;Acc:P42766] RPL35 0.231604586
5.6527 1957 1.30722 PROTEIN TRANSPORT PROTEIN SEC61 ALPHA SUBUNIT ISOFORM 2 (SEC61 ALPHA- 2). [SWISSPROT;Acc:Q9Y2R3] SEC61A2 0.23125586
5.69292 1430 1.38784 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] PSMA1 0.243783507
5.71481 1945 1.32337 60S RIBOSOMAL PROTEIN L26. [SWISSPROT;Acc:Q02877] RPL26 0.231568504
5.71513 1943 1.32362 40S RIBOSOMAL PROTEIN S15 (RIG PROTEIN). [SWISSPROT;Acc:P11174] no value 0.231599281
5.7155 1944 1.3237 MITOCHONDRIAL RIBOSOMAL PROTEIN L2. [RefSeq;Acc:NM_015950] MRPL2 0.231598285
5.73234 1954 1.32564 PROTEIN TRANSPORT PROTEIN SEC61 ALPHA SUBUNIT ISOFORM 1 (SEC61 ALPHA- 1). [SWISSPROT;Acc:P38378] SEC61A1 0.231256346
5.76236 1893 1.34083 60S RIBOSOMAL PROTEIN L3-LIKE. [SWISSPROT;Acc:Q92901] RPL3L 0.232687649
5.86431 1909 1.36156 MITOCHONDRIAL 60S RIBOSOMAL PROTEIN L3 (L3MT). [SWISSPROT;Acc:P09001] MRPL3 0.232177358
6.01339 3088 0.587123 CYTOPLASMIC DYNEIN LIGHT CHAIN (T-COMPLEX TESTIS-SPECIFIC PROTEIN 1 HOMOLOG) (PROTEIN CW-1). [SWISSPROT;Acc:Q15763] DYNLT1 0.097635942
6.05655 1934 1.40328 60S RIBOSOMAL PROTEIN L23A. [SWISSPROT;Acc:P29316] no value 0.231696263
6.12181 437 1.69676 EYES ABSENT HOMOLOG 2. [SWISSPROT;Acc:O00167] EYA2 0.277166394
6.13294 1968 1.41778 60S RIBOSOMAL PROTEIN L5. [SWISSPROT;Acc:P46777] RPL5 0.231174608
6.22802 404 1.73296 GENERAL VESICULAR TRANSPORT FACTOR P115 (TRANSCYTOSIS ASSOCIATED PROTEIN) (TAP) (VESICLE DOCKING PROTEIN). [SWISSPROT;Acc:O60763] USO1 0.278252157
6.30537 1339 1.5466 GTP BINDING PROTEIN 2. [RefSeq;Acc:NM_019096] GTPBP2 0.245282989
6.35074 436 1.76022 EYES ABSENT HOMOLOG 1. [SWISSPROT;Acc:Q99502] EYA1 0.2771677
6.35359 435 1.76157 EYES ABSENT HOMOLOG 4. [SWISSPROT;Acc:O95677] EYA4 0.277255851
6.36689 345 1.799 ALPHA-ACTININ 2 (ALPHA ACTININ SKELETAL MUSCLE ISOFORM 2) (F-ACTIN CROSS LINKING PROTEIN). [SWISSPROT;Acc:P35609] ACTN2 0.282555533
6.36963 2012 1.469 40S RIBOSOMAL PROTEIN S2 (S4) (LLREP3 PROTEIN). [SWISSPROT;Acc:P15880] no value 0.230625641
6.5312 1908 1.51643 40S RIBOSOMAL PROTEIN S3. [SWISSPROT;Acc:P23396] RPS3 0.232182447
6.64504 466 1.83106 LIM PROTEIN (SIMILAR TO RAT PROTEIN KINASE C-BINDING ENIGMA); ENIGMA HOMOLOG. [RefSeq;Acc:NM_006457] PDLIM5 0.275552894
6.77601 2046 1.55851 DNA-DIRECTED RNA POLYMERASE I 40 KDA POLYPEPTIDE (EC 2.7.7.6) (RPA40) (RPA39). [SWISSPROT;Acc:O15160] POLR1C 0.230004088
6.99164 2070 1.60424 DNA-DIRECTED RNA POLYMERASE II 33 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB3) (RNA POLYMERASE II SUBUNIT 3) (RPB33) (RPB31). [SWISSPROT;Acc:P19387] POLR2C 0.229451173
7.19846 291 2.17256 KELCH-LIKE PROTEIN 8. [SWISSPROT;Acc:Q9P2G9] KLHL8 0.301808998
7.43888 410 2.06651 EYES ABSENT HOMOLOG 3. [SWISSPROT;Acc:Q99504] EYA3 0.27779854
9.03714 458 2.49065 ZASP PROTEIN (FRAGMENT). [SPTREMBL;Acc:Q9Y4Z3] LDB3 0.275601573
11.3823 3167 0.73655 C5orf33 0.06471012
25.135 3139 1.64337 NSMCE4A 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/