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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Gene expected Rank description measured Hugo final
Results: HTML CSV LaTeX Showing element 551 to 600 of 3206 in total
expected
Rank
description
measured
Hugo
final
0.164816 371 DESTRIN (ACTIN-DEPOLYMERIZING FACTOR) (ADF). [SWISSPROT;Acc:P18282] 0.0460179 DSTN 0.279207723
372 "COFILIN, MUSCLE ISOFORM (COFILIN 2). [SWISSPROT;Acc:Q9Y281]" CFL2
0.164951 1156 0.0411817 CYB5D2 0.249660202
0.165025 1807 "EARLY ENDOSOME ANTIGEN 1, 162KD; EARLY ENDOSOME-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_003566]" 0.0387072 EEA1 0.234553552
0.165264 1956 60S RIBOSOMAL PROTEIN L34. [SWISSPROT;Acc:P49207] 0.0382183 RPL34 0.231256051
0.165297 2866 HEPATOMA-DERIVED GROWTH FACTOR-RELATED PROTEIN 2. [RefSeq;Acc:NM_032631] 0.0312313 no value 0.188940513
0.165745 127 ERO1-LIKE. [RefSeq;Acc:NM_014584] 0.0588477 0.355049624
0.165754 100 "INOSITOL POLYPHOSPHATE-4-PHOSPHATASE, TYPE 1 ISOFORM B; INOSITOL POLYPHOSPHATE-4-PHOSPHATASE, TYPE I, 107KD; 4-PHOSPHATASE I; INOSITOL POLYPHOSPHATE-4-PHOSPHATASE I. [RefSeq;Acc:NM_001566]" 0.0619579 INPP4A 0.373794298
0.165888 2870 HEPATOMA-DERIVED GROWTH FACTOR (HDGF) (HIGH-MOBILITY GROUP PROTEIN 1- LIKE 2) (HMG-1L2). [SWISSPROT;Acc:P51858] 0.0313429 HDGF 0.188940128
0.166067 102 "SELENIDE,WATER DIKINASE 1 (EC 2.7.9.3) (SELENOPHOSPHATE SYNTHETASE 1) (SELENIUM DONOR PROTEIN 1). [SWISSPROT;Acc:P49903]" 0.0620748 SEPHS1 0.37379371
0.166118 2346 THIOREDOXIN DOMAIN CONTAINING; THIOREDOXIN-RELATED TRANSMEMBRANE PROTEIN; THIOREDOXIN DOMAIN-CONTAINING. [RefSeq;Acc:NM_030755] 0.0366305 TXNDC1 0.220508915
0.166122 694 "ATP-BINDING CASSETTE, SUB-FAMILY D, MEMBER 3 (70 KDA PEROXISOMAL MEMBRANE PROTEIN) (PMP70). [SWISSPROT;Acc:P28288]" 0.0441291 ABCD3 0.26564272
0.16661 180 TRINUCLEOTIDE REPEAT CONTAINING 15. [RefSeq;Acc:NM_015575] 0.0561104 no value 0.336776904
0.166906 2994 HEPARAN SULFATE D-GLUCOSAMINYL 3-O-SULFOTRANSFERASE 3B1. [RefSeq;Acc:NM_006041] 0.0225884 HS3ST3B1 0.135336057
0.166987 1131 PYRIDOXINE 5'-PHOSPHATE OXIDASE. [RefSeq;Acc:NM_018129] 0.0418316 PNPO 0.250508123
0.167562 2424 ATP-DEPENDENT DNA HELICASE Q5 (RECQ PROTEIN-LIKE 5) (RECQ5). [SWISSPROT;Acc:O94762] 0.0365106 RECQL5 0.217893078
0.168127 1045 0.0425806 TMEM87A 0.253264496
0.168345 1270 HYPOXIA-INDUCIBLE FACTOR-3 ALPHA ISOFORM A; INHIBITORY PAS DOMAIN PROTEIN. [RefSeq;Acc:NM_152794] 0.0415296 HIF3A 0.246693397
0.1684 1960 PROTEIN 1-4 (ATP BINDING PROTEIN ASSOCIATED WITH CELL DIFFERENTIATION). [SWISSPROT;Acc:O14530] 0.0389372 TXNDC9 0.231218527
0.169175 2900 TRANSCRIPTION REPRESSOR P66 BETA COMPONENT OF THE MECP1 COMPLEX. [RefSeq;Acc:NM_020699] 0.0295551 GATAD2B 0.174701345
0.1694 1887 PEPTIDYL PROLYL ISOMERASE H; CYCLOPHILIN H. [RefSeq;Acc:NM_006347] 0.039427 PPIH 0.232744982
0.169541 1148 GBP PROTEIN ISOFORM A. [RefSeq;Acc:NM_017870] 0.0424223 TMEM132A 0.250218531
0.169567 2125 0.038682 TCP11L1 0.228122217
0.169647 862 0.0441578 PYROXD1 0.260292254
863 "RABAPTIN, RAB GTPASE BINDING EFFECTOR PROTEIN 1; RABAPTIN-5; NEUROCRESCIN. [RefSeq;Acc:NM_004703]" RABEP1
0.169867 1051 RNA (GUANINE-7-) METHYLTRANSFERASE. [RefSeq;Acc:NM_003799] 0.0429379 RNMT 0.252773641
0.169952 1050 CALNEXIN PRECURSOR (MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I ANTIGEN-BINDING PROTEIN P88) (P90) (IP90). [SWISSPROT;Acc:P27824] 0.0429594 CANX 0.252773724
0.170042 1311 0.0417836 SERBP1 0.245725174
0.170257 1340 SFRS PROTEIN KINASE 1; SR PROTEIN KINASE 1. [RefSeq;Acc:NM_003137] 0.0417611 SRPK1 0.24528272
1341 XAP-5 PROTEIN (HXC-26 PROTEIN). [SWISSPROT;Acc:Q14320] FAM50A
1342 SERINE/THREONINE PROTEIN KINASE 23 (EC 2.7.1.37) (MUSCLE-SPECIFIC SERINE KINASE 1) (MSSK-1). [SWISSPROT;Acc:Q9UPE1] SRPK3
1343 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-6 ALPHA (ACTIVATING TRANSCRIPTION FACTOR 6 ALPHA) (ATF6-ALPHA). [SWISSPROT;Acc:P18850] ATF6
0.170278 307 MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2B (MAD2-LIKE 2) (HREV7). [SWISSPROT;Acc:Q9UI95] 0.0503334 MAD2L2 0.295595438
308 MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S32 (S32MT) (MRP-S32) (PTD007) (HSPC204). [SWISSPROT;Acc:Q9Y6G3] no value
309 RBM42
0.170299 389 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN D2; RSC6P; MAMMALIAN CHROMATIN REMODELING COMPLEX BRG1-ASSOCIATED FACTOR 60B; SWP73-LIKE PROTEIN; CHROMATIN REMODELING COMPLEX BAF60B SUBUNIT; SWI/SNF COMPLEX 60 KDA SUBUNIT B. [Sour 0.0474703 SMARCD2 0.278746792
0.170469 1312 "3-HYDROXYANTHRANILATE 3,4-DIOXYGENASE (EC 1.13.11.6) (3-HAO) (3-HYDROXYANTHRANILIC ACID DIOXYGENASE) (3-HYDROXYANTHRANILATE OXYGENASE). [SWISSPROT;Acc:P46952]" 0.0418885 HAAO 0.245725029
1313 ZINC FINGER PROTEIN-LIKE 1; ZINC-FINGER PROTEIN IN MEN1 REGION. [RefSeq;Acc:NM_006782] ZFPL1
0.170682 1309 HOMEOBOX PROSPERO-LIKE PROTEIN PROX1 (PROX 1). [SWISSPROT;Acc:Q92786] 0.0419409 PROX1 0.245725384
0.171181 2654 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 3. [SWISSPROT;Acc:O14828] 0.0359383 SCAMP3 0.209943276
0.17129 2202 HEPARIN SULFATE N-DEACETYLASE/N-SULFOTRANSFERASE (EC 2.8.2.-) (N- HSST) (N-HEPARIN SULFATE SULFOTRANSFERASE) (GLUCOSAMINYL N- DEACETYLASE/N-SULFOTRANSFERASE). [SWISSPROT;Acc:P52849] 0.0386224 NDST2 0.225479596
0.171305 1219 0.0424937 WDR55 0.248058726
0.171674 356 0.0483186 no value 0.281455549
0.171772 2363 "SOLUTE CARRIER FAMILY 20 (PHOSPHATE TRANSPORTER), MEMBER 2; GLVR-2; PIT-2; GIBBON APE LEUKEMIA VIRUS RECEPTOR 2; MURINE LEUKEMIA VIRUS, AMPHOTROPIC; RECEPTOR. [RefSeq;Acc:NM_006749]" 0.0378408 SLC20A2 0.220296672
0.171872 1279 EPSIN 1; EH DOMAIN-BINDING MITOTIC PHOSPHOPROTEIN. [RefSeq;Acc:NM_013333] 0.0423484 EPN1 0.246394992
0.172112 989 CPG BINDING PROTEIN (PROTEIN CONTAINING PHD FINGER AND CXXC DOMAIN 1). [SWISSPROT;Acc:Q9P0U4] 0.0439174 CXXC1 0.255167565
0.172225 380 CALCYPHOSINE. [SWISSPROT;Acc:Q13938] 0.0480742 CAPS 0.279136014
0.172299 403 CENTAURIN GAMMA 2. [SWISSPROT;Acc:Q9UPQ3] 0.0479426 CENTG2 0.27825234
0.172385 2888 DIPEPTIDYL PEPTIDASE 8 ISOFORM 2; DIPEPTIDYL PEPTIDASE 8. [RefSeq;Acc:NM_017743] 0.0310206 DPP8 0.179949532
0.172653 549 SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH PROTEIN (SH3BGR PROTEIN) (21- GLUTAMIC ACID-RICH PROTEIN) (21-GARP). [SWISSPROT;Acc:P55822] 0.046789 SH3BGR 0.271000214

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/