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 [...,...].
expected description Rank Hugo final Gene measured
Results: HTML CSV LaTeX Showing element 2658 to 2707 of 3206 in total
expected
description
Rank
Hugo
final
measured
1.48829 RIBULOSE-5-PHOSPHATE-3-EPIMERASE; RIBULOSE 5-PHOSPHATE 3-EPIMERASE. [RefSeq;Acc:NM_006916] 2372 no value 0.220049184 0.327497
1.48848 RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (RAF-1) (C-RAF). [SWISSPROT;Acc:P04049] 2955 RAF1 0.147639202 0.219758
1.49161 2755 SSU72 0.203634998 0.303744
1.49174 MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A (MAD2-LIKE 1) (HSMAD2). [SWISSPROT;Acc:Q13257] 1190 MAD2L1 0.248602303 0.37085
1.49189 "KARYOPHERIN BETA 2B, TRANSPORTIN; IMPORTIN 3. [RefSeq;Acc:NM_013433]" 532 TNPO2 0.271387971 0.404881
1.49271 CAD PROTEIN [INCLUDES: GLUTAMINE-DEPENDENT CARBAMOYL-PHOSPHATE SYNTHASE (EC 6.3.5.5); ASPARTATE CARBAMOYLTRANSFERASE (EC 2.1.3.2); DIHYDROOROTASE (EC 3.5.2.3)]. [SWISSPROT;Acc:P27708] 2083 CAD 0.229024392 0.341867
1.49288 40S RIBOSOMAL PROTEIN S13. [SWISSPROT;Acc:Q02546] 1897 RPS13 0.232570602 0.3472
1.49712 HEPATOCYTE NUCLEAR FACTOR 3-ALPHA (HNF-3A) (FORKHEAD BOX PROTEIN A1). [SWISSPROT;Acc:P55317] 580 FOXA1 0.270110612 0.404388
1.5 XPA BINDING PROTEIN 1; MBD2 INTERACTOR PROTEIN; PUTATIVE ATP(GTP)-BINDING PROTEIN. [RefSeq;Acc:NM_007266] 11 XAB1 0.542592 0.813888
1.50518 TRANSCRIPTION INITIATION FACTOR TFIID 100 KDA SUBUNIT (TAFII-100) (TAFII100). [SWISSPROT;Acc:Q15542] 2368 TAF5 0.220147756 0.331362
1.50657 C-TERMINAL BINDING PROTEIN 2 (CTBP2). [SWISSPROT;Acc:P56545] 738 CTBP2 0.264639545 0.398698
1.50787 CYSTEINE ENDOPEPTIDASE AUT-LIKE 2 ISOFORM A; AUTOPHAGY-RELATED CYSTEINE ENDOPEPTIDASE 2; AUTOPHAGIN 2. [RefSeq;Acc:NM_052936] 3067 ATG4A 0.103512902 0.156084
1.50997 TYROSINE-PROTEIN KINASE FRK (EC 2.7.1.112) (NUCLEAR TYROSINE PROTEIN KINASE RAK). [SWISSPROT;Acc:P42685] 27 FRK 0.426117737 0.643425
1.51127 "VACUOLAR ATP SYNTHASE SUBUNIT B, BRAIN ISOFORM (EC 3.6.3.14) (V-ATPASE B2 SUBUNIT) (VACUOLAR PROTON PUMP B ISOFORM 2) (ENDOMEMBRANE PROTON PUMP 58 KDA SUBUNIT) (HO57). [SWISSPROT;Acc:P21281]" 1744 ATP6V1B2 0.236717463 0.357744
1.51635 AUTOPHAGY PROTEIN 5-LIKE (APG5-LIKE) (APOPTOSIS-SPECIFIC PROTEIN). [SWISSPROT;Acc:Q9H1Y0] 653 ATG5 0.267820754 0.40611
1.5203 FARNESYL PYROPHOSPHATE SYNTHETASE (FPP SYNTHETASE) (FPS) (FARNESYL DIPHOSPHATE SYNTHETASE) [INCLUDES: DIMETHYLALLYLTRANSFERASE (EC 2.5.1.1); GERANYLTRANSTRANSFERASE (EC 2.5.1.10)]. [SWISSPROT;Acc:P14324] 2365 FDPS 0.220296652 0.334917
1.52156 ARP2/3 COMPLEX 16 KDA SUBUNIT (P16-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 5). [SWISSPROT;Acc:O15511] 717 ARPC5 0.264795999 0.402903
1.52661 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1 (EC 5.2.1.8) (ROTAMASE PIN1) (PPIASE PIN1). [SWISSPROT;Acc:Q13526] 2139 PIN1 0.22782374 0.347798
1.52927 TRANSFORMING PROTEIN P21/H-RAS-1 (C-H-RAS). [SWISSPROT;Acc:P01112] 2961 HRAS 0.146163856 0.223524
1.5325 BIFUNCTIONAL AMINOACYL-TRNA SYNTHETASE [INCLUDES: GLUTAMYL-TRNA SYNTHETASE (EC 6.1.1.17) (GLUTAMATE--TRNA LIGASE); PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE)]. [SWISSPROT;Acc:P07814] 2353 EPRS 0.220368026 0.337714
1.53626 "PYRUVATE DEHYDROGENASE E1 COMPONENT ALPHA SUBUNIT, TESTIS-SPECIFIC FORM, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-A TYPE II). [SWISSPROT;Acc:P29803]" 2030 PDHA2 0.230296304 0.353795
1.53719 "ADENYLATE KINASE ISOENZYME 4, MITOCHONDRIAL (EC 2.7.4.3) (ATP-AMP TRANSPHOSPHORYLASE). [SWISSPROT;Acc:P27144]" 1967 no value 0.231217351 0.355425
1.53743 HEPATOCYTE NUCLEAR FACTOR 3-BETA (HNF-3B) (FORKHEAD BOX PROTEIN A2). [SWISSPROT;Acc:Q9Y261] 596 FOXA2 0.269294862 0.414022
1.54054 CLATHRIN COAT ASSEMBLY PROTEIN AP50 (CLATHRIN COAT ASSOCIATED PROTEIN AP50) (PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN) (HA2 50 KDA SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 MEDIUM CHAIN) (AP-2 MU 2 CHAIN). [SWISSPROT;Acc:P20172] 2912 AP2M1 0.174141535 0.268272
1.54946 "PROBABLE DIMETHYLADENOSINE TRANSFERASE (EC 2.1.1.-) (S- ADENOSYLMETHIONINE-6-N',N'-ADENOSYL(RRNA) DIMETHYLTRANSFERASE) (18S RRNA DIMETHYLASE). [SWISSPROT;Acc:Q9UNQ2]" 1722 DIMT1L 0.237161334 0.367472
1.55176 PUTATIVE SIALOGLYCOPROTEASE TYPE 2. [RefSeq;Acc:NM_022353] 1783 OSGEPL1 0.235285096 0.365106
1.55221 "EGF-LIKE-DOMAIN, MULTIPLE 7; NEU1 PROTEIN. [RefSeq;Acc:NM_016215]" 3124 EGFL7 0.075688857 0.117485
1.55638 60S RIBOSOMAL PROTEIN L18. [SWISSPROT;Acc:Q07020] 2132 RPL18 0.227977743 0.35482
1.55794 RNA-BINDING PROTEIN 9 (RNA BINDING MOTIF PROTEIN 9) (HEXARIBONUCLEOTIDE BINDING PROTEIN 2) (REPRESSOR OF TAMOXIFEN TRANSCRIPTIONAL ACTIVITY). [SWISSPROT;Acc:O43251] 514 RBM9 0.27250536 0.424547
1.55897 DIPHTHAMIDE BIOSYNTHESIS-LIKE PROTEIN 2. [RefSeq;Acc:NM_001384] 2278 DPH2 0.222553994 0.346955
1.56247 125 C9orf41 0.357121097 0.557991
1.56343 CYTOPLASMIC PROTEIN NCK2 (NCK ADAPTOR PROTEIN 2) (SH2/SH3 ADAPTOR PROTEIN NCK-BETA) (NCK-2). [SWISSPROT;Acc:O43639] 268 NCK2 0.307242409 0.480352
1.56403 EUKARYOTIC TRANSLATION INITIATION FACTOR 5A (EIF-5A) (EIF-4D) (REV- BINDING FACTOR). [SWISSPROT;Acc:P10159] 1586 EIF5AP1 0.24075817 0.376553
1.57686 WD-REPEAT PROTEIN 3. [SWISSPROT;Acc:Q9UNX4] 1454 WDR3 0.243150311 0.383414
1.57699 GERM CELL-LESS. [RefSeq;Acc:NM_022471] 1060 no value 0.25263762 0.398407
1.57827 DYNACTIN COMPLEX 50 KDA SUBUNIT (50 KDA DYNEIN-ASSOCIATED POLYPEPTIDE) (DYNAMITIN) (DCTN-50) (DYNACTIN 2). [SWISSPROT;Acc:Q13561] 1694 DCTN2 0.237869946 0.375423
1.57878 "BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.42) (BCAT(M)) (PLACENTAL PROTEIN 18) (PP18). [SWISSPROT;Acc:O15382]" 1452 BCAT2 0.243340427 0.384181
1.58875 NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA (NF-Y PROTEIN CHAIN C) (NUCLEAR FACTOR YC) (NF-YC) (CCAAT-BINDING TRANSCRIPTION FACTOR SUBUNIT C) (CBF-C) (TRANSACTIVATOR HSM-1/2). [SWISSPROT;Acc:Q13952] 3115 NFYC 0.090676318 0.144062
1.59051 HEMK PROTEIN HOMOLOG (EC 2.1.1.-) (M.HSAHEMKP). [SWISSPROT;Acc:Q9Y5R4] 2484 HEMK1 0.216265852 0.343973
1.59398 CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 4. [RefSeq;Acc:NM_030627] 3071 CPEB4 0.103197029 0.164494
1.59695 NUCLEOSIDE DIPHOSPHATE KINASE 3 (EC 2.7.4.6) (NDK 3) (NDP KINASE 3) (NM23-H3) (DR-NM23). [SWISSPROT;Acc:Q13232] 2065 NME3 0.229464291 0.366443
1.59883 APG3P; PC3-96 PROTEIN. [RefSeq;Acc:NM_022488] 3000 ATG3 0.128961803 0.206188
1.59982 XPA-BINDING PROTEIN 2 (HCNP PROTEIN) (PP3898). [SWISSPROT;Acc:Q9HCS7] 451 XAB2 0.27604418 0.441621
1.60336 KH-TYPE SPLICING REGULATORY PROTEIN (FUSE BINDING PROTEIN 2); KH-TYPE SPLICING REGULATORY PROTEIN (FUSE-BINDING PROTEIN 2). [RefSeq;Acc:NM_003685] 833 KHSRP 0.260980067 0.418445
1.60341 HELICASE (FRAGMENT). [SPTREMBL;Acc:Q92771] 2767 no value 0.202098029 0.324046
1.60405 719 ARPC5L 0.264769178 0.424703
1.60594 CDC42-INTERACTING PROTEIN 4 (THYROID RECEPTOR INTERACTING PROTEIN 10) (TRIP-10). [SWISSPROT;Acc:Q15642] 384 TRIP10 0.279042804 0.448126
1.60666 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM2 (SMALL NUCLEAR RIBONUCLEAR PROTEIN D HOMOLOG) (G7B) (SNRNP CORE SM-LIKE PROTEIN SM-X5). [SWISSPROT;Acc:Q9Y333] 1487 no value 0.242827979 0.390142
1.60733 CDA11 PROTEIN. [RefSeq;Acc:NM_032026] 1777 TATDN1 0.235579501 0.378654
1.61155 GUANYLATE KINASE (EC 2.7.4.8) (GMP KINASE). [SWISSPROT;Acc:Q16774] 2392 GUK1 0.219554466 0.353823

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/