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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank expected description measured Hugo final
Results: HTML CSV LaTeX Showing element 1602 to 1651 of 3206 in total
Rank
expected
description
measured
Hugo
final
1602 0.130205 POLYGLUTAMINE BINDING PROTEIN 1; NUCLEAR PROTEIN CONTAINING WW DOMAIN 38 KD. [RefSeq;Acc:NM_005710] 0.0312503 PQBP1 0.240008448
1603 0.567058 ADENYLYL CYCLASE-ASSOCIATED PROTEIN 1 (CAP 1). [SWISSPROT;Acc:Q01518] 0.136076 CAP1 0.239968398
1604 0.292225 60S RIBOSOMAL PROTEIN L28. [SWISSPROT;Acc:P46779] 0.0701119 RPL28 0.239924373
1605 3.51976 PROTEIN BAP28. [SWISSPROT;Acc:Q9H583] 0.844333 HEATR1 0.239883685
1606 0.967917 0.232181 KATNAL1 0.239876973
1607 0.551914 ADENYLYL CYCLASE-ASSOCIATED PROTEIN 2 (CAP 2). [SWISSPROT;Acc:P40123] 0.132388 CAP2 0.239870704
1608 0.183648 KATANIN P80 SUBUNIT B 1; KATANIN (80 KDA); KATANIN P80 (WD40-CONTAINING) SUBUNIT B 1. [RefSeq;Acc:NM_005886] 0.0440508 KATNB1 0.239865395
1609 0.64258 KATANIN P60 SUBUNIT A 1. [RefSeq;Acc:NM_007044] 0.154124 KATNA1 0.239851847
1610 1.24282 UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 1 ISOFORM B; DNA-BINDING PROTEIN. [RefSeq;Acc:NM_003349] 0.298042 TMEM189 0.239811075
1611 0.847819 UTP--GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE 2 (EC 2.7.7.9) (UDP- GLUCOSE PYROPHOSPHORYLASE 2) (UDPGP 2) (UGPASE 2). [SWISSPROT;Acc:Q16851] 0.203313 UGP2 0.239807081
1612 1.14341 "UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2; 1 ALPHA,25-DIHYDROXYVITAMIN D3-INDUCIBLE; ENTEROCYTE DIFFERENTIATION PROMOTING FACTOR; METHYL METHANESULFONATE SENSITIVE 2, S. CEREVISIAE, HOMOLOG OF. [RefSeq;Acc:NM_003350]" 0.274194 UBE2V2 0.239803745
1613 0.161954 MITOCHONDRIAL RIBOSOMAL PROTEIN L30 ISOFORM A. [RefSeq;Acc:NM_145212] 0.0388254 MRPL30 0.239731035
1614 4.96583 26S PROTEASE REGULATORY SUBUNIT S10B (PROTEASOME SUBUNIT P42) (P44) (CONSERVED ATPASE DOMAIN PROTEIN 44) (CADP44). [SWISSPROT;Acc:Q92524] 1.19046 PSMC6 0.239730317
1615 0.641812 0.153801 C20orf11 0.239635594
1616 0.160453 0.0384502 MAEA 0.239635283
1617 RMND5A
1618 0.35015 ACID CERAMIDASE PRECURSOR (EC 3.5.1.23) (ACYLSPHINGOSINE DEACYLASE) (N-ACYLSPHINGOSINE AMIDOHYDROLASE) (AC) (PUTATIVE 32 KDA HEART PROTEIN) (PHP32). [SWISSPROT;Acc:Q13510] 0.083902 ASAH1 0.239617307
1619 0.063934 OLIGOPHRENIN 1. [SWISSPROT;Acc:O60890] 0.0153184 OPHN1 0.239597084
1620 0.302259 SENESCENCE MARKER PROTEIN-30 (SMP-30) (REGUCALCIN) (RC). [SWISSPROT;Acc:Q15493] 0.0724203 RGN 0.239596836
1621 0.62682 "CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL PRECURSOR (CYTOCHROME C-1). [SWISSPROT;Acc:P08574]" 0.150184 CYC1 0.239596694
1622 0.0850893 OLIGOPHRENIN-1 LIKE PROTEIN (GTPASE REGULATOR ASSOCIATED WITH FOCAL ADHESION KINASE). [SWISSPROT;Acc:Q9UNA1] 0.0203871 ARHGAP26 0.239596518
1623 0.0681463 0.0163276 ARHGAP10 0.23959628
1624 1.40952 CAMP-DEPENDENT PROTEIN KINASE TYPE II-BETA REGULATORY CHAIN. [SWISSPROT;Acc:P31323] 0.337407 PRKAR2B 0.239377235
1625 0.598798 PROTEIN KINASE PKX1 (EC 2.7.1.-). [SWISSPROT;Acc:P51817] 0.143332 PRKX 0.239366197
1626 0.796037 "CAMP-DEPENDENT PROTEIN KINASE, GAMMA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-GAMMA). [SWISSPROT;Acc:P22612]" 0.190544 PRKACG 0.239365758
1627 0.880269 "CAMP-DEPENDENT PROTEIN KINASE, BETA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-BETA). [SWISSPROT;Acc:P22694]" 0.210706 PRKACB 0.239365467
1628 "CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-ALPHA). [SWISSPROT;Acc:P17612]" PRKACA
1629 1.63914 CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA REGULATORY CHAIN. [SWISSPROT;Acc:P13861] 0.392337 PRKAR2A 0.239355394
1630 0.551746 0.132038 PHLPPL 0.239309392
1631 0.699345 0.167352 PHLPP 0.2392982
1632 1.19135 TRIPARTITE MOTIF PROTEIN 2. [SWISSPROT;Acc:Q9C040] 0.285075 TRIM2 0.239287363
1633 3.92552 0.938982 KIAA0368 0.239199393
1634 0.384447 INOSITOL-1(OR 4)-MONOPHOSPHATASE 2 (EC 3.1.3.25) (IMPASE 2) (IMP 2) (INOSITOL MONOPHOSPHATASE 2) (MYO-INOSITOL MONOPHOSPHATASE A2). [SWISSPROT;Acc:O14732] 0.0919591 IMPA2 0.239198381
1635 0.461922 INOSITOL-1(OR 4)-MONOPHOSPHATASE (EC 3.1.3.25) (IMPASE) (IMP) (INOSITOL MONOPHOSPHATASE) (LITHIUM-SENSITIVE MYO-INOSITOL MONOPHOSPHATASE A1). [SWISSPROT;Acc:P29218] 0.110487 IMPA1 0.239189733
1636 0.64312 MITOTIC CHECKPOINT PROTEIN BUB3. [SWISSPROT;Acc:O43684] 0.153821 BUB3 0.239179313
1637 0.32156 ZINC FINGER PROTEIN 207. [SWISSPROT;Acc:O43670] 0.0769103 ZNF207 0.239178691
1638 3.20427 26S PROTEASE REGULATORY SUBUNIT 6A (TAT-BINDING PROTEIN 1) (TBP-1) (PROTEASOME SUBUNIT P50). [SWISSPROT;Acc:P17980] 0.766353 PSMC3 0.239166175
1639 3.30538 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 7 (26S PROTEASOME REGULATORY SUBUNIT S12) (PROTEASOME SUBUNIT P40) (MOV34 PROTEIN HOMOLOG). [SWISSPROT;Acc:P51665] 0.790323 PSMD7 0.239102009
1640 0.301896 ALPHA-FETOPROTEIN ENHANCER BINDING PROTEIN (AT MOTIF-BINDING FACTOR) (AT-BINDING TRANSCRIPTION FACTOR 1). [SWISSPROT;Acc:Q15911] 0.0721691 ZFHX3 0.239052853
1641 0.422881 UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A (HHR23A). [SWISSPROT;Acc:P54725] 0.101079 RAD23A 0.23902469
1642 0.204356 0.0488461 no value 0.239024545
1643 0.2611 0.0624093 DDI1 0.239024512
1644 5.30247 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 PSMD4 0.239024455
1645 0.514211 UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG B (HHR23B) (XP-C REPAIR COMPLEMENTING COMPLEX 58 KDA PROTEIN) (P58). [SWISSPROT;Acc:P54727] 0.122909 RAD23B 0.239024447
1646 0.210535 MYOSIN VI. [SWISSPROT;Acc:Q9UM54] 0.050323 no value 0.23902439
1647 0.11537 0.0275762 0.23902401
1648 0.23248 INOSITOL POLYPHOSPHATE 5-PHOSPHATASE OCRL-1 (EC 3.1.3.36) (LOWE'S OCULOCEREBRORENAL SYNDROME PROTEIN). [SWISSPROT;Acc:Q01968] 0.0555683 OCRL 0.239024002
1649 1.47667 0.352885 COQ5 0.238973501
1650 0.142333 "CHAPERONE-ACTIVITY OF BC1 COMPLEX-LIKE, MITOCHONDRIAL PRECURSOR (CHAPERONE-ABC1-LIKE). [SWISSPROT;Acc:Q8NI60]" 0.0340138 CABC1 0.238973393
1651 AARF DOMAIN CONTAINING KINASE 1. [RefSeq;Acc:NM_020421] ADCK1

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/