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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Rank Gene Hugo description measured expected final
Results: HTML CSV LaTeX Showing element 252 to 301 of 350 in total
Hugo  : no value
Rank
description
measured
expected
final
2326 SERPIN B11. [SWISSPROT;Acc:Q96P15] 0.0194204 0.0875599 0.221795594
2331 40S RIBOSOMAL PROTEIN S27 (METALLOPAN-STIMULIN 1) (MPS-1). [SWISSPROT;Acc:P42677] 0.228054 1.0307 0.221261279
2347 0.1385 0.628094 0.220508395
2366 PEPSIN A PRECURSOR (EC 3.4.23.1). [SWISSPROT;Acc:P00790] 0.0604093 0.274218 0.220296625
2372 RIBULOSE-5-PHOSPHATE-3-EPIMERASE; RIBULOSE 5-PHOSPHATE 3-EPIMERASE. [RefSeq;Acc:NM_006916] 0.327497 1.48829 0.220049184
2375 THIAMIN PYROPHOSPHOKINASE 1; MOUSE THIAMIN PYROPHOSPHOKINASE HOMOLOG; THIAMINE PYROPHOSPHOKINASE. [RefSeq;Acc:NM_022445] 0.0258973 0.117689 0.220048603
2394 "BLOOM'S SYNDROME PROTEIN (EC 3.6.1.-) (RECQ PROTEIN-LIKE 3) (DNA HELICASE, RECQ-LIKE, TYPE 2). [SWISSPROT;Acc:P54132]" 0.106596 0.485769 0.219437634
2401 WILLIAMS-BEUREN SYNDROME CRITICAL REGION PROTEIN 20 COPY B. [RefSeq;Acc:NM_145645] 0.0801834 0.366045 0.219053395
2404 REPRESSOR OF ESTROGEN RECEPTOR ACTIVITY; B-CELL ASSOCIATED PROTEIN. [RefSeq;Acc:NM_007273] 0.26817 1.22481 0.218948245
2409 0.112482 0.514239 0.218734868
2413 0.030828500000000002 0.141189 0.218349163
2423 TRANSCRIPTION ELONGATION FACTOR A PROTEIN 1 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 1) (TRANSCRIPTION ELONGATION FACTOR TFIIS.O). [SWISSPROT;Acc:P23193] 0.0637011 0.29203 0.218132041
2435 MICROSOMAL SIGNAL PEPTIDASE 18 KDA SUBUNIT (EC 3.4.-.-) (SPASE 18 KDA SUBUNIT) (SPC18) (ENDOPEPTIDASE SP18). [SWISSPROT;Acc:P21378] 0.157677 0.725721 0.217269447
2441 MYO-INOSITOL 1-PHOSPHATE SYNTHASE A1. [RefSeq;Acc:NM_016368] 0.0388043 0.178742 0.217096709
2443 ARSENICAL PUMP-DRIVING ATPASE (EC 3.6.3.16) (ARSENITE-TRANSLOCATING ATPASE) (ARSENICAL RESISTANCE ATPASE) (ARSENITE-TRANSPORTING ATPASE) (ARSA) (ASNA-I). [SWISSPROT;Acc:O43681] 0.539817 2.48653 0.217096516
2446 LARGE PROLINE-RICH PROTEIN BAT3 (HLA-B-ASSOCIATED TRANSCRIPT 3) (G3). [SWISSPROT;Acc:P46379] 0.109079 0.502445 0.217096399
2489 0.194172 0.898593 0.216084479
2492 0.239571 1.11109 0.215617997
2502 KERATIN ASSOCIATED PROTEIN 9-4; KERATIN ASSOCIATED PROTEIN 9.4. [RefSeq;Acc:NM_033191] 1.02862 4.7857 0.214936164
2507 ALPHA-PARVIN (CALPONIN-LIKE INTEGRIN-LINKED KINASE BINDING PROTEIN) (CH-ILKBP). [SWISSPROT;Acc:Q9NVD7] 0.0405241 0.188688 0.214767765
2521 KERATIN ASSOCIATED PROTEIN 4-12; KERATIN ASSOCIATED PROTEIN 4.12. [RefSeq;Acc:NM_031854] 0.042399 0.19742 0.214765475
2522 0.0436957 0.203458 0.21476521
2525 KERATIN ASSOCIATED PROTEIN 4.9 (FRAGMENT). [SPTREMBL;Acc:Q9BYQ8] 0.0383264 0.178458 0.214764258
2526 KERATIN ASSOCIATED PROTEIN 4-14; KERATIN ASSOCIATED PROTEIN 4.14. [RefSeq;Acc:NM_033059] 0.0382656 0.178175 0.214764136
2528 KERATIN ASSOCIATED PROTEIN 4-2; KERATIN ASSOCIATED PROTEIN 4.2. [RefSeq;Acc:NM_033062] 0.0314375 0.146383 0.21476196
2529 KERATIN ASSOCIATED PROTEIN 4-10; KERATIN ASSOCIATED PROTEIN 4.10. [RefSeq;Acc:NM_033060] 0.0280741 0.130722 0.214761861
2530 "KERATIN, ULTRA HIGH-SULFUR MATRIX PROTEIN A (UHS KERATIN A) (UHS KERA). [SWISSPROT;Acc:P26371]" 0.0250957 0.116854 0.214761155
2531 KERATIN ASSOCIATED PROTEIN 1-3; KERATIN ASSOCIATED PROTEIN 1.3. [RefSeq;Acc:NM_030966] 0.0258656 0.120439 0.214760999
2532 KERATIN ASSOCIATED PROTEIN 1.5. [RefSeq;Acc:NM_031957] 0.0249741 0.116288 0.214760766
2533 KERATIN ASSOCIATED PROTEIN 2-4; KERATIN ASSOCIATED PROTEIN 2.4. [RefSeq;Acc:NM_033184] 0.0240826 0.112137 0.214760516
2534 KERATIN ASSOCIATED PROTEIN 4.3 (FRAGMENT). [SPTREMBL;Acc:Q9BYR4] 0.0260682 0.121383 0.214759892
2541 0.0217565 0.101375 0.214614057
2552 "DNA TOPOISOMERASE II, ALPHA ISOZYME (EC 5.99.1.3). [SWISSPROT;Acc:P11388]" 0.286606 1.33628 0.214480498
2553 0.0511995 0.238723 0.214472422
2555 METABOTROPIC GLUTAMATE RECEPTOR 3 PRECURSOR (MGLUR3). [SWISSPROT;Acc:Q14832] 0.0333153 0.155451 0.214313835
2565 TETRATRICOPEPTIDE REPEAT PROTEIN 4 (MY044 PROTEIN). [SWISSPROT;Acc:O95801] 0.061947 0.290115 0.213525671
2566 3-HYDROXYISOBUTYRYL-COENZYME A HYDROLASE. [RefSeq;Acc:NM_014362] 0.512064 2.39827 0.213513908
2574 0.0577101 0.270506 0.213341294
2580 BLOOD GROUP RH(CE) POLYPEPTIDE (RHESUS C/E ANTIGENS) (RH30A) (RHIXB) (RH POLYPEPTIDE 1) (RHPI). [SWISSPROT;Acc:P18577] 0.0564693 0.264963 0.213121455
2582 0.0561617 0.26352 0.213121205
2590 DC11 PROTEIN. [RefSeq;Acc:NM_020186] 0.0255653 0.120086 0.212891594
2592 HEPATITIS C VIRUS CORE-BINDING PROTEIN 6; CERVICAL CANCER ONCOGENE 3. [RefSeq;Acc:NM_023934]
2619 ALCOHOL DEHYDROGENASE CLASS III CHI CHAIN (EC 1.1.1.1) (GLUTATHIONE- DEPENDENT FORMALDEHYDE DEHYDROGENASE) (EC 1.2.1.1) (FDH). [SWISSPROT;Acc:P11766] 0.478004 2.27081 0.210499337
2666 NEURAL CELL ADHESION MOLECULE L1 PRECURSOR (N-CAM L1) (CD171 ANTIGEN). [SWISSPROT;Acc:P32004] 0.02527 0.120774 0.209233775
2670 TRANSCRIPTION FACTOR MAFG (V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG G) (HMAF). [SWISSPROT;Acc:O15525] 0.0798317 0.381544 0.209233273
2672 TRANSCRIPTION FACTOR MAFK (ERYTHROID TRANSCRIPTION FACTOR NF-E2 P18 SUBUNIT). [SWISSPROT;Acc:O60675] 0.0897053 0.428734 0.209232998
2677 GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE (EC 2.7.7.12) (GAL-1-P URIDYLYLTRANSFERASE) (UDP-GLUCOSE--HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE). [SWISSPROT;Acc:P07902] 0.0454701 0.217847 0.208724931
2698 ESTROGEN-RELATED RECEPTOR GAMMA (ESTROGEN RECEPTOR RELATED PROTEIN 3) (ERR GAMMA-2). [SWISSPROT;Acc:O75454] 0.151787 0.730409 0.207810966
2707 0.542979 2.61855 0.207358653
2716 0.411399 1.98421 0.207336421

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/