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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description Rank measured Gene expected Hugo final
Results: HTML CSV LaTeX Showing element 51 to 100 of 350 in total
Hugo  : no value
description
Rank
measured
expected
final
2275 0.294007 1.32025 0.2226904
2306 0.25396 1.14298 0.222191114
2347 0.1385 0.628094 0.220508395
2409 0.112482 0.514239 0.218734868
2413 0.030828500000000002 0.141189 0.218349163
2489 0.194172 0.898593 0.216084479
2492 0.239571 1.11109 0.215617997
2522 0.0436957 0.203458 0.21476521
2541 0.0217565 0.101375 0.214614057
2553 0.0511995 0.238723 0.214472422
2574 0.0577101 0.270506 0.213341294
2707 0.542979 2.61855 0.207358653
2716 0.411399 1.98421 0.207336421
2723 0.0313747 0.1519 0.206548387
2725 0.10808 0.525053 0.205845886
2807 0.101691 0.514373 0.197698946
2872 0.0371369 0.196598 0.188897649
3069 0.0533885 0.517345 0.103197093
"4-AMINOBUTYRATE AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.19) (GAMMA-AMINO-N-BUTYRATE TRANSAMINASE) (GABA TRANSAMINASE) (GABA AMINOTRANSFERASE) (GABA-AT) (GABA-T). [SWISSPROT;Acc:P80404]" 2115 0.16968 0.743642 0.22817431
"40S RIBOSOMAL PROTEIN S4, X ISOFORM (SINGLE COPY ABUNDANT MRNA PROTEIN) (SCR10). [SWISSPROT;Acc:P12750]" 2040 0.707942 3.07604 0.230147202
"ACYL-COA DEHYDROGENASE, SHORT/BRANCHED CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.-) (SBCAD) (2-METHYL BRANCHED CHAIN ACYL-COA DEHYDROGENASE) (2-MEBCAD) (2-METHYLBUTYRYL-COENZYME A DEHYDROGENASE) (2-METHYLBUTYRYL-COA DEHYDROGENASE). [SWISSP" 960 0.0614814 0.240043 0.256126611
"ADENYLATE KINASE ISOENZYME 4, MITOCHONDRIAL (EC 2.7.4.3) (ATP-AMP TRANSPHOSPHORYLASE). [SWISSPROT;Acc:P27144]" 1967 0.355425 1.53719 0.231217351
"ATAXIN 2; OLIVOPONTOCEREBELLAR ATAXIA 2, AUTOSOMAL DOMINANT. [RefSeq;Acc:NM_002973]" 2799 0.0572133 0.287777 0.198811232
"ATP-DEPENDENT DNA HELICASE II, 70 KDA SUBUNIT (LUPUS KU AUTOANTIGEN PROTEIN P70) (KU70) (70 KDA SUBUNIT OF KU ANTIGEN) (THYROID-LUPUS AUTOANTIGEN) (TLAA) (CTC BOX BINDING FACTOR 75 KDA SUBUNIT) (CTCBF) (CTC75). [SWISSPROT;Acc:P12956]" 1040 0.0397033 0.156754 0.253284127
"BETA-CAROTENE DIOXYGENASE 2; PUTATIVE B,B-CAROTENE-9',10'-DIOXYGENASE. [RefSeq;Acc:NM_031938]" 294 0.0429558 0.142328 0.301808499
"BLOOM'S SYNDROME PROTEIN (EC 3.6.1.-) (RECQ PROTEIN-LIKE 3) (DNA HELICASE, RECQ-LIKE, TYPE 2). [SWISSPROT;Acc:P54132]" 2394 0.106596 0.485769 0.219437634
"CASEIN KINASE I, EPSILON ISOFORM (EC 2.7.1.-) (CKI-EPSILON) (CKIE). [SWISSPROT;Acc:P49674]" 2233 0.273568 1.22019 0.224201149
"CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL PRECURSOR (EC 2.7.3.2) (U- MTCK) (MIA-CK) (ACIDIC-TYPE MITOCHONDRIAL CREATINE KINASE). [SWISSPROT;Acc:P12532]" 1882 0.199469 0.856983 0.232757243
"DJ681N20.2 (NOVEL PROTEIN SIMILAR TO FERRITIN, LIGHT POLYPEPTIDE (FTL)). [SPTREMBL;Acc:Q9BYW6]" 58 0.0511645 0.124441 0.411154684
"DJ850E9.1 (NOVEL C2H2 TYPE ZINC FINGER PROTEIN SIMILAR TO DROSOPHILA SCRATCH (SCRT), SLUG AND XENOPUS SNAIL) (FRAGMENT). [SPTREMBL;Acc:Q9NQ03]" 1766 0.281698 1.1936 0.236007038
"DNA TOPOISOMERASE II, ALPHA ISOZYME (EC 5.99.1.3). [SWISSPROT;Acc:P11388]" 2552 0.286606 1.33628 0.214480498
"FATTY ACID-BINDING PROTEIN, EPIDERMAL (E-FABP) (PSORIASIS-ASSOCIATED FATTY ACID-BINDING PROTEIN HOMOLOG) (PA-FABP). [SWISSPROT;Acc:Q01469]" 287 0.0334849 0.110947 0.301809873
"GLYCEROL KINASE, TESTIS SPECIFIC 1 (EC 2.7.1.30) (ATP:GLYCEROL 3- PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:Q14409]" 2272 0.131767 0.591632 0.222717838
"GLYCEROL KINASE, TESTIS SPECIFIC 2 (EC 2.7.1.30) (ATP:GLYCEROL 3- PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:Q14410]" 2273 0.137099 0.615573 0.222717696
"GLYCINE CLEAVAGE SYSTEM H PROTEIN, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:P23434]" 2180 0.207889 0.916816 0.22675106
"GLYCINE DEHYDROGENASE [DECARBOXYLATING], MITOCHONDRIAL PRECURSOR (EC 1.4.4.2) (GLYCINE DECARBOXYLASE) (GLYCINE CLEAVAGE SYSTEM P- PROTEIN). [SWISSPROT;Acc:P23378]" 2127 0.0640341 0.280704 0.228119656
"ISOLEUCYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.5) (ISOLEUCINE--TRNA LIGASE) (ILERS) (IRS). [SWISSPROT;Acc:P41252]" 1940 0.0589414 0.254478 0.231616878
"KERATIN, ULTRA HIGH-SULFUR MATRIX PROTEIN A (UHS KERATIN A) (UHS KERA). [SWISSPROT;Acc:P26371]" 2530 0.0250957 0.116854 0.214761155
"LON PROTEASE HOMOLOG, MITOCHONDRIAL PRECURSOR (EC 3.4.21.-) (LON PROTEASE-LIKE PROTEIN) (LONP) (LONHS). [SWISSPROT;Acc:P36776]" 2021 0.0840355 0.364571 0.230505169
"MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE IB (EC 3.2.1.113) (PROCESSING ALPHA-1,2-MANNOSIDASE IB) (ALPHA-1,2-MANNOSIDASE IB) (MANNOSIDASE ALPHA CLASS 1A MEMBER 2). [SWISSPROT;Acc:O60476]" 3109 0.116081 1.26306 0.091904581
"MYOSIN HEAVY CHAIN, CARDIAC MUSCLE ALPHA ISOFORM (MYHC-ALPHA). [SWISSPROT;Acc:P13533]" 3166 0.081705 1.26263 0.064710168
"MYOSIN HEAVY CHAIN, CARDIAC MUSCLE BETA ISOFORM (MYHC-BETA). [SWISSPROT;Acc:P12883]" 3163 0.0816437 1.26168 0.064710307
"MYOSIN LIGHT CHAIN 1, EMBRYONIC MUSCLE/ATRIAL ISOFORM (PRO1957). [SWISSPROT;Acc:P12829]" 820 0.0259096 0.0991465 0.261326421
"MYOSIN VA (MYOSIN 5A) (DILUTE MYOSIN HEAVY CHAIN, NON-MUSCLE) (MYOSIN HEAVY CHAIN 12) (MYOXIN). [SWISSPROT;Acc:Q9Y4I1]" 3131 0.163856 2.39209 0.068499095
"PEROXISOMAL 3,2-TRANS-ENOYL-COA ISOMERASE (EC 5.3.3.8) (DODECENOYL-COA DELTA-ISOMERASE) (D3,D2-ENOYL-COA ISOMERASE) (DBI-RELATED PROTEIN 1) (DRS-1) (HEPATOCELLULAR CARCINOMA-ASSOCIATED ANTIGEN 88). [SWISSPROT;Acc:O75521]" 2119 0.745512 3.26763 0.228150678
"PRE-MRNA CLEAVAGE FACTOR I, 59 KDA SUBUNIT. [RefSeq;Acc:NM_024811]" 522 0.694134 2.5522 0.271974767
"PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14C; SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-81; PKC-POTENTIATED PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_030949]" 3187 0.028817 0.772261 0.037315105
"PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 (EC 3.1.3.48) (PROTEIN-TYROSINE PHOSPHATASE 1B) (PTP-1B). [SWISSPROT;Acc:P18031]" 452 0.215243 0.779889 0.27599184
"SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, ALPHA ISOFORM (PP2A, SUBUNIT B, B-ALPHA ISOFORM) (PP2A, SUBUNIT B, B55-ALPHA ISOFORM) (PP2A, SUBUNIT B, PR55-ALPHA ISOFORM) (PP2A, SUBUNIT B, R2-ALPHA ISOFORM). [SWISSPROT;Acc:Q0" 582 0.0948257 0.351165 0.270031751
"SH2 DOMAIN BINDING PROTEIN 1; TPR-CONTAINING, SH2-BINDING PHOSPHOPROTEIN. [RefSeq;Acc:NM_014633]" 1165 0.144652 0.579965 0.249415051

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/