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 [...,...].
Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1608 to 1657 of 3206 in total
Rank
description
measured
expected
final
Hugo
1608 KATANIN P80 SUBUNIT B 1; KATANIN (80 KDA); KATANIN P80 (WD40-CONTAINING) SUBUNIT B 1. [RefSeq;Acc:NM_005886] 0.0440508 0.183648 0.239865395 KATNB1
1609 KATANIN P60 SUBUNIT A 1. [RefSeq;Acc:NM_007044] 0.154124 0.64258 0.239851847 KATNA1
1610 UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 1 ISOFORM B; DNA-BINDING PROTEIN. [RefSeq;Acc:NM_003349] 0.298042 1.24282 0.239811075 TMEM189
1611 UTP--GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE 2 (EC 2.7.7.9) (UDP- GLUCOSE PYROPHOSPHORYLASE 2) (UDPGP 2) (UGPASE 2). [SWISSPROT;Acc:Q16851] 0.203313 0.847819 0.239807081 UGP2
1612 "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 1.14341 0.239803745 UBE2V2
1613 MITOCHONDRIAL RIBOSOMAL PROTEIN L30 ISOFORM A. [RefSeq;Acc:NM_145212] 0.0388254 0.161954 0.239731035 MRPL30
1614 26S PROTEASE REGULATORY SUBUNIT S10B (PROTEASOME SUBUNIT P42) (P44) (CONSERVED ATPASE DOMAIN PROTEIN 44) (CADP44). [SWISSPROT;Acc:Q92524] 1.19046 4.96583 0.239730317 PSMC6
1615 0.153801 0.641812 0.239635594 C20orf11
1616 0.0384502 0.160453 0.239635283 MAEA
1617 RMND5A
1618 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 0.35015 0.239617307 ASAH1
1619 OLIGOPHRENIN 1. [SWISSPROT;Acc:O60890] 0.0153184 0.063934 0.239597084 OPHN1
1620 SENESCENCE MARKER PROTEIN-30 (SMP-30) (REGUCALCIN) (RC). [SWISSPROT;Acc:Q15493] 0.0724203 0.302259 0.239596836 RGN
1621 "CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL PRECURSOR (CYTOCHROME C-1). [SWISSPROT;Acc:P08574]" 0.150184 0.62682 0.239596694 CYC1
1622 OLIGOPHRENIN-1 LIKE PROTEIN (GTPASE REGULATOR ASSOCIATED WITH FOCAL ADHESION KINASE). [SWISSPROT;Acc:Q9UNA1] 0.0203871 0.0850893 0.239596518 ARHGAP26
1623 0.0163276 0.0681463 0.23959628 ARHGAP10
1624 CAMP-DEPENDENT PROTEIN KINASE TYPE II-BETA REGULATORY CHAIN. [SWISSPROT;Acc:P31323] 0.337407 1.40952 0.239377235 PRKAR2B
1625 PROTEIN KINASE PKX1 (EC 2.7.1.-). [SWISSPROT;Acc:P51817] 0.143332 0.598798 0.239366197 PRKX
1626 "CAMP-DEPENDENT PROTEIN KINASE, GAMMA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-GAMMA). [SWISSPROT;Acc:P22612]" 0.190544 0.796037 0.239365758 PRKACG
1627 "CAMP-DEPENDENT PROTEIN KINASE, BETA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-BETA). [SWISSPROT;Acc:P22694]" 0.210706 0.880269 0.239365467 PRKACB
1628 "CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-ALPHA). [SWISSPROT;Acc:P17612]" PRKACA
1629 CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA REGULATORY CHAIN. [SWISSPROT;Acc:P13861] 0.392337 1.63914 0.239355394 PRKAR2A
1630 0.132038 0.551746 0.239309392 PHLPPL
1631 0.167352 0.699345 0.2392982 PHLPP
1632 TRIPARTITE MOTIF PROTEIN 2. [SWISSPROT;Acc:Q9C040] 0.285075 1.19135 0.239287363 TRIM2
1633 0.938982 3.92552 0.239199393 KIAA0368
1634 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 0.384447 0.239198381 IMPA2
1635 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 0.461922 0.239189733 IMPA1
1636 MITOTIC CHECKPOINT PROTEIN BUB3. [SWISSPROT;Acc:O43684] 0.153821 0.64312 0.239179313 BUB3
1637 ZINC FINGER PROTEIN 207. [SWISSPROT;Acc:O43670] 0.0769103 0.32156 0.239178691 ZNF207
1638 26S PROTEASE REGULATORY SUBUNIT 6A (TAT-BINDING PROTEIN 1) (TBP-1) (PROTEASOME SUBUNIT P50). [SWISSPROT;Acc:P17980] 0.766353 3.20427 0.239166175 PSMC3
1639 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 7 (26S PROTEASOME REGULATORY SUBUNIT S12) (PROTEASOME SUBUNIT P40) (MOV34 PROTEIN HOMOLOG). [SWISSPROT;Acc:P51665] 0.790323 3.30538 0.239102009 PSMD7
1640 ALPHA-FETOPROTEIN ENHANCER BINDING PROTEIN (AT MOTIF-BINDING FACTOR) (AT-BINDING TRANSCRIPTION FACTOR 1). [SWISSPROT;Acc:Q15911] 0.0721691 0.301896 0.239052853 ZFHX3
1641 UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A (HHR23A). [SWISSPROT;Acc:P54725] 0.101079 0.422881 0.23902469 RAD23A
1642 0.0488461 0.204356 0.239024545 no value
1643 0.0624093 0.2611 0.239024512 DDI1
1644 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 5.30247 0.239024455 PSMD4
1645 UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG B (HHR23B) (XP-C REPAIR COMPLEMENTING COMPLEX 58 KDA PROTEIN) (P58). [SWISSPROT;Acc:P54727] 0.122909 0.514211 0.239024447 RAD23B
1646 MYOSIN VI. [SWISSPROT;Acc:Q9UM54] 0.050323 0.210535 0.23902439 no value
1647 0.0275762 0.11537 0.23902401
1648 INOSITOL POLYPHOSPHATE 5-PHOSPHATASE OCRL-1 (EC 3.1.3.36) (LOWE'S OCULOCEREBRORENAL SYNDROME PROTEIN). [SWISSPROT;Acc:Q01968] 0.0555683 0.23248 0.239024002 OCRL
1649 0.352885 1.47667 0.238973501 COQ5
1650 "CHAPERONE-ACTIVITY OF BC1 COMPLEX-LIKE, MITOCHONDRIAL PRECURSOR (CHAPERONE-ABC1-LIKE). [SWISSPROT;Acc:Q8NI60]" 0.0340138 0.142333 0.238973393 CABC1
1651 AARF DOMAIN CONTAINING KINASE 1. [RefSeq;Acc:NM_020421] ADCK1
1652 AARF DOMAIN CONTAINING KINASE 2; PUTATIVE UBIQUINONE BIOSYNTHESIS PROTEIN AARF. [RefSeq;Acc:NM_052853] ADCK2
1653 AARF DOMAIN CONTAINING KINASE 4. [RefSeq;Acc:NM_024876] 0.0274831 0.115005 0.238973088 ADCK4
1654 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 13 (26S PROTEASOME REGULATORY SUBUNIT S11) (26S PROTEASOME REGULATORY SUBUNIT P40.5). [SWISSPROT;Acc:Q9UNM6] 0.75685 3.16764 0.238931823 PSMD13
1655 APURINIC/APYRIMIDINIC ENDONUCLEASE 2; APURINIC/APYRIMIDINIC ENDONUCLEASE-LIKE 2; APEX NUCLEASE-LIKE 2. [RefSeq;Acc:NM_014481] 0.0730689 0.305877 0.238883277 APEX2
1656 COPPER-TRANSPORTING ATPASE 1 (EC 3.6.3.4) (COPPER PUMP 1) (MENKES DISEASE-ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q04656] 0.0806616 0.337708 0.238850131 ATP7A
1657 CYCLIN M2; ANCIENT CONSERVED DOMAIN PROTEIN 2. [RefSeq;Acc:NM_017649] 0.317455 1.3291 0.238849597 CNNM2

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/