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