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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measured Gene Rank description Hugo expected final
Results: HTML CSV LaTeX Showing element 351 to 400 of 3206 in total
measured
Rank
description
Hugo
expected
final
0.0319827 2650 VACUOLAR PROTEIN SORTING 35 (VESICLE PROTEIN SORTING 35) (HVPS35) (MATERNAL-EMBRYONIC 3). [SWISSPROT;Acc:Q96QK1] VPS35 0.152326 0.209962186
0.0319993 2561 "28S RIBOSOMAL PROTEIN S18A, MITOCHONDRIAL PRECURSOR (MRP-S18-A) (MRPS18A) (MRP-S18-3). [SWISSPROT;Acc:Q9NVS2]" MRPS18A 0.149576 0.213933385
0.0320251 2527 KERATIN ASSOCIATED PROTEIN 4.4. [RefSeq;Acc:NM_032524] KRTAP4-4 0.149118 0.214763476
0.032048 3046 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-8 SUBUNIT (GAMMA-9). [SWISSPROT;Acc:Q9UK08] GNG8 0.300389 0.106688327
0.0320499 2001 POLY (ADP-RIBOSE) GLYCOHYDROLASE. [RefSeq;Acc:NM_003631] no value 0.138898 0.230744143
0.0320568 2975 HOMEOBOX PROTEIN HOX-C5 (HOX-3D) (CP11). [SWISSPROT;Acc:Q00444] HOXC5 0.2297 0.139559425
0.0321572 752 LIPOPOLYSACCHARIDE-RESPONSIVE AND BEIGE-LIKE ANCHOR PROTEIN (CDC4-LIKE PROTEIN) (BEIGE-LIKE PROTEIN). [SWISSPROT;Acc:P50851] no value 0.121579 0.264496336
0.032182 1446 SPERMIDINE SYNTHASE (EC 2.5.1.16) (PUTRESCINE AMINOPROPYLTRANSFERASE) (SPDSY). [SWISSPROT;Acc:P19623] SRM 0.132186 0.243459973
0.0322443 2334 RIBOSOME BIOGENESIS REGULATORY PROTEIN HOMOLOG. [SWISSPROT;Acc:Q15050] RRS1 0.145754 0.221224117
0.0322794 1099 PHOSPHOGLYCERATE MUTASE 1 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (PHOSPHOGLYCERATE MUTASE ISOZYME B) (PGAM-B) (BPG-DEPENDENT PGAM 1). [SWISSPROT;Acc:P18669] no value 0.128445 0.251309121
0.0322816 2293 TROPOMODULIN 1 (ERYTHROCYTE TROPOMODULIN) (E-TMOD). [SWISSPROT;Acc:P28289] TMOD1 0.145189 0.222341913
2294 ACTIVATED P21CDC42HS KINASE. [RefSeq;Acc:NM_005781] TNK2
0.0322934 1168 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 2 (SMAD 2) (MOTHERS AGAINST DPP HOMOLOG 2) (MAD-RELATED PROTEIN 2) (HMAD-2) (JV18-1) (HSMAD2). [SWISSPROT;Acc:Q15796] SMAD2 0.129486 0.249396846
0.0323264 2008 "HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 2 (EC 2.1.1.43) (HISTONE H3-K9 METHYLTRANSFERASE 2) (H3-K9-HMTASE 2) (SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 2) (SU(VAR)3-9 HOMOLOG 2). [SWISSPROT;Acc:Q9H5I1]" SUV39H2 0.14013 0.230688646
0.0324086 1092 3-OXO-5-ALPHA-STEROID 4-DEHYDROGENASE 2 (EC 1.3.99.5) (STEROID 5-ALPHA-REDUCTASE 2) (SR TYPE 2) (5 ALPHA-SR2). [SWISSPROT;Acc:P31213] SRD5A2 0.12882 0.2515805
0.0325023 3013 FRY 0.266776 0.121833673
0.032514 1692 "ADP,ATP CARRIER PROTEIN, FIBROBLAST ISOFORM (ADP/ATP TRANSLOCASE 2) (ADENINE NUCLEOTIDE TRANSLOCATOR 2) (ANT 2). [SWISSPROT;Acc:P05141]" SLC25A5 0.136688 0.237870186
1693 "ADP,ATP CARRIER PROTEIN, HEART/SKELETAL MUSCLE ISOFORM T1 (ADP/ATP TRANSLOCASE 1) (ADENINE NUCLEOTIDE TRANSLOCATOR 1) (ANT 1). [SWISSPROT;Acc:P12235]" SLC25A4
0.0325155 925 FATTY ACID DESATURASE 3; LINOLEOYL-COA DESATURASE (DELTA-6-DESATURASE)-LIKE 3; DELTA-6 FATTY ACID DESATURASE. [RefSeq;Acc:NM_021727] FADS3 0.126186 0.25767914
0.0325606 2107 FBXO42 0.142608 0.228322394
0.0325717 1767 THYROID RECEPTOR INTERACTING PROTEIN 12 (TRIP12). [SWISSPROT;Acc:Q14669] TRIP12 0.138013 0.236004579
0.0326222 2908 SAP30L 0.187331 0.174142027
2909 "ATP-BINDING CASSETTE, SUB-FAMILY C, MEMBER 10; MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN 7. [RefSeq;Acc:NM_033450]" ABCC10
0.0326245 1697 ASPARAGINE SYNTHETASE [GLUTAMINE-HYDROLYZING] (EC 6.3.5.4) (GLUTAMINE- DEPENDENT ASPARAGINE SYNTHETASE) (TS11 CELL CYCLE CONTROL PROTEIN). [SWISSPROT;Acc:P08243] ASNS 0.137154 0.237867652
0.0326359 2203 HEPARAN SULFATE N-DEACETYLASE/N-SULFOTRANSFERASE (EC 2.8.2.8) (N-HSST) (HSNST) ([HEPARAN SULFATE]-GLUCOSAMINE N-SULFOTRANSFERASE) (N-HEPARAN SULFATE SULFOTRANSFERASE) (GLUCOSAMINYL N-DEACETYLASE/N- SULFOTRANSFERASE). [SWISSPROT;Acc:P52848] NDST1 0.14474 0.22547948
0.0326423 1169 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 3 (SMAD 3) (MOTHERS AGAINST DPP HOMOLOG 3) (MAD3) (HMAD-3) (MMAD3) (JV15-2) (HSMAD3). [SWISSPROT;Acc:Q92940] SMAD3 0.130885 0.249396799
0.0326969 3045 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-3 SUBUNIT. [SWISSPROT;Acc:P29798] GNG3 0.306454 0.106694316
0.0327033 2026 C3orf23 0.142004 0.230298442
0.0327294 1043 TMEM87B 0.12923 0.253264722
0.0328245 3044 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-4 SUBUNIT. [SWISSPROT;Acc:P50150] GNG4 0.307647 0.106695336
0.0328701 755 CCDC93 0.124442 0.264139921
0.0329569 2456 TRANSCRIPTION FACTOR 8 (NIL-2-A ZINC FINGER PROTEIN) (NEGATIVE REGULATOR OF IL2). [SWISSPROT;Acc:P37275] ZEB1 0.15207 0.216721904
0.0330141 711 F-ACTIN CAPPING PROTEIN ALPHA-3 SUBUNIT (CAPZ ALPHA-3) (GERM CELL- SPECIFIC PROTEIN 3). [SWISSPROT;Acc:Q96KX2] CAPZA3 0.124574 0.265015974
0.0330661 1499 IMPORTIN 8; RAN-BINDING PROTEIN 8. [RefSeq;Acc:NM_006390] IPO8 0.1362 0.242776065
0.0331306 2622 MITOGEN-ACTIVATED PROTEIN KINASE 12 (EC 2.7.1.37) (EXTRACELLULAR SIGNAL-REGULATED KINASE 6) (ERK-6) (ERK5) (STRESS-ACTIVATED PROTEIN KINASE-3) (MITOGEN-ACTIVATED PROTEIN KINASE P38 GAMMA) (MAP KINASE P38 GAMMA). [SWISSPROT;Acc:P53778] MAPK11 0.157765 0.209999683
0.0331615 1852 PRESENILIN-LIKE PROTEIN 1 (EC 3.4.99.-) (SPPL2B PROTEIN). [SWISSPROT;Acc:Q8TCT7] no value 0.142049 0.233451133
1853
0.0331688 1336 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-6 BETA (ACTIVATING TRANSCRIPTION FACTOR 6 BETA) (ATF6-BETA) (CAMP RESPONSIVE ELEMENT BINDING PROTEIN-LIKE 1) (CAMP RESPONSE ELEMENT BINDING PROTEIN-RELATED PROTEIN) (CREB-RP) (G13 PROTEIN). [SWISSPROT;A CREBL1 0.135226 0.245284191
0.0332619 2237 "ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT GAMMA, MITOCHONDRIAL PRECURSOR (EC 1.1.1.41) (ISOCITRIC DEHYDROGENASE) (NAD+-SPECIFIC ICDH). [SWISSPROT;Acc:P51553]" IDH3G 0.14849299999999999 0.223996417
0.0333011 1314 "PROLYL 4-HYDROXYLASE ALPHA-1 SUBUNIT PRECURSOR (EC 1.14.11.2) (4-PH ALPHA-1) (PROCOLLAGEN-PROLINE,2-OXOGLUTARATE-4-DIOXYGENASE ALPHA-1 SUBUNIT). [SWISSPROT;Acc:P13674]" P4HA1 0.135522 0.245724679
0.0333153 2555 METABOTROPIC GLUTAMATE RECEPTOR 3 PRECURSOR (MGLUR3). [SWISSPROT;Acc:Q14832] no value 0.155451 0.214313835
2556 C1orf26
0.0333753 1020 HIV TAT SPECIFIC FACTOR 1; COFACTOR REQUIRED FOR TAT ACTIVATION OF HIV-1 TRANSCRIPTION. [RefSeq;Acc:NM_014500] HTATSF1 0.131474 0.253854755
0.0334849 287 "FATTY ACID-BINDING PROTEIN, EPIDERMAL (E-FABP) (PSORIASIS-ASSOCIATED FATTY ACID-BINDING PROTEIN HOMOLOG) (PA-FABP). [SWISSPROT;Acc:Q01469]" no value 0.110947 0.301809873
0.0335632 1306 HYALURONAN BINDING PROTEIN 4; INTRACELLULAR ANTIGEN DETECTED BY MONOCLONAL ANTIBODY KI-1; INTRACELLULAR HYALURONAN-BINDING PROTEIN; CHROMODOMAIN HELICASE DNA BINDING PROTEIN 3 INTERACTING PROTEIN. [RefSeq;Acc:NM_014282] HABP4 0.136588 0.245725832
0.0335839 1671 MIER2 0.140652 0.238773
0.0336801 928 FATTY ACID DESATURASE 2; LINOLEOYL-COA DESATURASE (DELTA-6-DESATURASE)-LIKE 2; DELTA-6 FATTY ACID DESATURASE. [RefSeq;Acc:NM_004265] FADS2 0.130706 0.257678301
0.0336981 1670 MIER3 0.14113 0.238773471
0.0336999 1521 ASC-1 COMPLEX SUBUNIT P100. [RefSeq;Acc:NM_032204] ASCC2 0.139062 0.242337231
0.0337015 2461 RPAP1 0.155511 0.216714573

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/