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 description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1358 to 1407 of 3206 in total
Rank
description
measured
expected
final
Hugo
1358 ELONGATION FACTOR 1-ALPHA 1 (EF-1-ALPHA-1) (ELONGATION FACTOR 1 A-1) (EEF1A-1) (ELONGATION FACTOR TU) (EF-TU). [SWISSPROT;Acc:P04720] 0.14659 0.598119 0.245085008 EEF1AL3
1359 MYB-RELATED PROTEIN A (A-MYB). [SWISSPROT;Acc:P10243] 0.106233 0.433454 0.24508483 MYBL1
1360 PROTEASOME SUBUNIT BETA TYPE 5 PRECURSOR (EC 3.4.25.1) (PROTEASOME EPSILON CHAIN) (MACROPAIN EPSILON CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX EPSILON CHAIN) (PROTEASOME SUBUNIT X) (PROTEASOME CHAIN 6) (PROTEASOME SUBUNIT MB1). [SWISSPROT;Acc:P2 0.779006 3.17883 0.245060604 PSMB5
1361 TRANSLATION INITIATION FACTOR IF-2. [SWISSPROT;Acc:O60841] 0.588043 2.39991 0.245027105 EIF5B
1362 0.596229 2.43411 0.244947435 no value
1363 ATP-DEPENDENT RNA HELICASE DDX24 (DEAD-BOX PROTEIN 24). [SWISSPROT;Acc:Q9GZR7] 0.230116 0.939561 0.244918638 DDX24
1364 HISTONE H2B.C (H2B/C). [SWISSPROT;Acc:Q99880] 0.0938754 0.38338 0.244862538 HIST1H2BL
1365 HISTONE H2B.D (H2B/D). [SWISSPROT;Acc:Q99877] 0.0957148 0.390892 0.24486252 no value
1366 "TESTIS-SPECIFIC HISTONE H2B; H2B HISTONE FAMILY, MEMBER U, (TESTIS-SPECIFIC). [RefSeq;Acc:NM_170610]" 0.0836563 0.341646 0.244862519 HIST1H2BA
1367 HISTONE H2B.E (H2B/E). [SWISSPROT;Acc:Q99879] 0.0942586 0.384945 0.244862513 no value
1368 HISTONE H3.1 (H3/A) (H3/C) (H3/D) (H3/F) (H3/H) (H3/I) (H3/J) (H3/K) (H3/L). [SWISSPROT;Acc:P16106] 0.157068 0.641454 0.244862453
1369 HISTONE H2B.Q (H2B/Q) (H2B-GL105). [SWISSPROT;Acc:Q16778] 0.0960725 0.392353 0.244862407 HIST2H2BA
1370 HISTONE H2B.S (H2B/S). [SWISSPROT;Acc:P57053] 0.0946163 0.386406 0.244862399 no value
1371 HISTONE H2B. [RefSeq;Acc:NM_175055] 0.0943097 0.385154 0.244862315
1372 HISTONE H3.4 (H3T) (H3/T) (H3/G). [SWISSPROT;Acc:Q16695] 0.147768 0.603475 0.244861842 HIST3H3
1373 0.403732 1.64923 0.244800301 ARID4B
1374 MKI67 (FHA DOMAIN) INTERACTING NUCLEOLAR PHOSPHOPROTEIN; NUCLEOLAR PHOSPHOPROTEIN NOPP34; NUCLEOLAR PROTEIN INTERACTING WITH THE FHA DOMAIN OF PKI-67. [RefSeq;Acc:NM_032390] 0.467786 1.91164 0.244704024 MKI67IP
1375 PROTEASOME SUBUNIT ALPHA TYPE 2 (EC 3.4.25.1) (PROTEASOME COMPONENT C3) (MACROPAIN SUBUNIT C3) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C3). [SWISSPROT;Acc:P25787] 1.02216 4.1775 0.244682226 PSMA2
1376 0.149037 0.609191 0.244647409 C14orf129
1377 HOMEOBOX PROTEIN PRH (HEMATOPOIETICALLY EXPRESSED HOMEOBOX) (HOMEOBOX PROTEIN HEX). [SWISSPROT;Acc:Q03014] 0.18361 0.750509 0.244647299 HHEX
1378 GLYCOGEN SYNTHASE KINASE-3 BETA (EC 2.7.1.37) (GSK-3 BETA). [SWISSPROT;Acc:P49841] 0.034279 0.140116 0.244647292 GSK3B
1379 "SUPPRESSOR OF VAR1, 3-LIKE 1. [RefSeq;Acc:NM_003171]" 0.0439474 0.179636 0.244646953 SUPV3L1
1380 BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-1 (BCL-2 BINDING ATHANOGENE- 1) (BAG-1) (GLUCOCORTICOID RECEPTOR-ASSOCIATED PROTEIN RAP46). [SWISSPROT;Acc:Q99933] 0.200609 0.819994 0.244646912 BAG1
1381 GLYCOGEN SYNTHASE KINASE-3 ALPHA (EC 2.7.1.37) (GSK-3 ALPHA). [SWISSPROT;Acc:P49840] 0.0268629 0.109803 0.244646321 GSK3A
1382 0.191835 0.784198 0.24462572 DDX55
1383 ATAXIN-1 UBIQUITIN-LIKE INTERACTING PROTEIN. [RefSeq;Acc:NM_020131] 0.427194 1.74675 0.244565049 UBQLN4
1384 UBIQUILIN 1 ISOFORM 1. [RefSeq;Acc:NM_013438] 0.508151 2.0779 0.244550267 UBQLN1
1385 AUTOANTIGEN NGP-1. [SWISSPROT;Acc:Q13823] 0.28719 1.17469 0.244481523 GNL2
1386 BA271B5.1 (SIMILAR TO RIBOSOMAL PROTEIN S7). [SPTREMBL;Acc:Q9H1S9] 0.037776 0.154523 0.244468461 no value
1387 APOLIPOPROTEIN B-100 PRECURSOR (APO B-100) [CONTAINS: APOLIPOPROTEIN B-48 (APO B-48)]. [SWISSPROT;Acc:P04114] 0.0307397 0.125741 0.244468391 APOB
1388 40S RIBOSOMAL PROTEIN S7 (S8). [SWISSPROT;Acc:P23821] 0.038293 0.156638 0.244468137 RPS7
1389 26S PROTEASOME-ASSOCIATED PAD1 HOMOLOG. [RefSeq;Acc:NM_005805] 1.1639 4.76096 0.244467502 PSMD14
1390 0.410655 1.68007 0.244427316 no value
1391 TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3 [INCLUDES: PHOSPHORIBOSYLAMINE--GLYCINE LIGASE (EC 6.3.4.13) (GARS) (GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE) (PHOSPHORIBOSYLGLYCINAMIDE SYNTHETASE); PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE (EC 6. 0.131799 0.53927 0.244402618 GART
1392 0.038432 0.157255 0.244392865 WDR82
1393 0.336304 1.37608 0.244392768 ABCF3
1394 UBIQUITIN-CONJUGATING ENZYME E2 A (EC 6.3.2.19) (UBIQUITIN-PROTEIN LIGASE A) (UBIQUITIN CARRIER PROTEIN A) (HR6A) (HHR6A). [SWISSPROT;Acc:P49459] 0.240046 0.982761 0.244256742 UBE2A
1395 MYOSIN VIIA. [SWISSPROT;Acc:Q13402] 0.066057 0.270441 0.244256603 MYO7A
1396 UBIQUITIN-CONJUGATING ENZYME E2 B (EC 6.3.2.19) (UBIQUITIN-PROTEIN LIGASE B) (UBIQUITIN CARRIER PROTEIN B) (HR6B) (HHR6B) (E2-17 KDA). [SWISSPROT;Acc:P23567] 0.222353 0.910326 0.244256453 UBE2B
1397 EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 3 (EUKARYOTIC TRANSLATION INITIATION FACTOR 2 GAMMA SUBUNIT) (EIF-2-GAMMA). [SWISSPROT;Acc:P41091] 0.361623 1.48057 0.244245797 EIF2S3
1398 MEGF6 (FRAGMENT). [SPTREMBL;Acc:O75095] 0.11514 0.471496 0.244201435 MEGF6
1399 0.0746708 0.305803 0.244179423 LSG1
1400 PROTEASOME SUBUNIT ALPHA TYPE 4 (EC 3.4.25.1) (PROTEASOME COMPONENT C9) (MACROPAIN SUBUNIT C9) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C9) (PROTEASOME SUBUNIT L). [SWISSPROT;Acc:P25789] 0.529846 2.17049 0.244113541 PSMA4
1401 DOUBLECORTIN (LISSENCEPHALIN-X) (LIS-X) (DOUBLIN). [SWISSPROT;Acc:O43602] 0.303311 1.24261 0.244091871 DCX
1402 0.15625 0.640129 0.244091425 FBXO28
1403 EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 2 (EUKARYOTIC TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT) (EIF-2-BETA). [SWISSPROT;Acc:P20042] 0.291311 1.19358 0.244064914 EIF2S2
1404 EPSIN 3. [RefSeq;Acc:NM_017957] 0.0468234 0.191876 0.244029477 EPN3
1405 FRAGILE X MENTAL RETARDATION 1 PROTEIN (PROTEIN FMR-1) (FMRP). [SWISSPROT;Acc:Q06787] 0.354424 1.45239 0.244028119 FMR1
1406 CYTOCHROME C. [SWISSPROT;Acc:P00001] 0.0314533 0.128904 0.244005617 CYCS
1407 HEPARAN SULFATE 6-O-SULFOTRANSFERASE; HEPARAN-SULFATE 6-SULFOTRANSFERASE. [RefSeq;Acc:NM_004807] HS6ST1

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/