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 Rank Gene description Hugo expected final
Results: HTML CSV LaTeX Showing element 2458 to 2507 of 3206 in total
measured
Rank
description
Hugo
expected
final
0.281309 501 SPECTRIN SH3 DOMAIN BINDING PROTEIN 1; EPS8 BINDING PROTEIN; INTERACTOR PROTEIN ABLBP4; ABL-INTERACTOR PROTEIN 1 LONG; NAP1 BINDING PROTEIN. [RefSeq;Acc:NM_005470] ABI1 1.0262 0.274126876
0.281345 208 ANDROGEN-INDUCED 1; CGI-103 PROTEIN; ANDROGEN INDUCED PROTEIN. [RefSeq;Acc:NM_016108] AIG1 0.87768 0.320555328
0.281375 971 SUPPRESSOR OF ACTIN MUTATIONS 2-LIKE ISOFORM B; DJ1033B10.5. [RefSeq;Acc:NM_022553] VPS52 1.10102 0.255558482
0.281519 8 ODD-SKIPPED RELATED 1; ODZ (ODD OZ/TEN-M) RELATED 1. [RefSeq;Acc:NM_145260] OSR1 0.487701 0.577236873
0.281682 612 CALCIPRESSIN 2 (THYROID HORMONE-RESPONSIVE PROTEIN ZAKI-4) (DOWN SYNDROME CANDIDATE REGION 1-LIKE 1) (MYOCYTE-ENRICHED CALCINEURIN INTERACTING PROTEIN 2) (MCIP2). [SWISSPROT;Acc:Q14206] RCAN2 1.04775 0.268844667
0.281698 1766 "DJ850E9.1 (NOVEL C2H2 TYPE ZINC FINGER PROTEIN SIMILAR TO DROSOPHILA SCRATCH (SCRT), SLUG AND XENOPUS SNAIL) (FRAGMENT). [SPTREMBL;Acc:Q9NQ03]" no value 1.1936 0.236007038
0.281828 1142 "TUMOR NECROSIS FACTOR, ALPHA-INDUCED PROTEIN 1, ENDOTHELIAL (B12 PROTEIN). [SWISSPROT;Acc:Q13829]" TNFAIP1 1.12603 0.250284628
0.282136 993 AFG3-LIKE PROTEIN 2 (EC 3.4.24.-) (PARAPLEGIN-LIKE PROTEIN). [SWISSPROT;Acc:Q9Y4W6] AFG3L2 1.10619 0.255052025
0.282189 2985 "BETA-ARRESTIN 1 (ARRESTIN, BETA 1). [SWISSPROT;Acc:P49407]" ARRB1 2.04196 0.138195165
0.28264 59 DISKS LARGE-ASSOCIATED PROTEIN 3 (DAP-3) (SAP90/PSD-95-ASSOCIATED PROTEIN 3) (SAPAP3) (PSD-95/SAP90 BINDING PROTEIN 3) (FRAGMENT). [SWISSPROT;Acc:O95886] DLGAP3 0.68743 0.41115459
0.28274 2245 "ATP SYNTHASE GAMMA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P36542]" ATP5C1 1.26423 0.223646014
2246 "ATP SYNTHASE OLIGOMYCIN SENSITIVITY CONFERRAL PROTEIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14) (OSCP). [SWISSPROT;Acc:P48047]" ATP5O
0.282811 1029 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE M2 CHAIN (EC 1.17.4.1) (RIBONUCLEOTIDE REDUCTASE SMALL CHAIN). [SWISSPROT;Acc:P31350] RRM2 1.11593 0.253430771
0.282831 2094 no value 1.23673 0.228692601
0.283008 1238 TBP-ASSOCIATED FACTOR 172 (TAF-172) (TAF(II)170). [SWISSPROT;Acc:O14981] BTAF1 1.14255 0.247698569
0.283215 620 "SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, ALPHA ISOFORM (EC 3.1.3.16) (CALMODULIN-DEPENDENT CALCINEURIN A SUBUNIT, ALPHA ISOFORM) (CAM-PRP CATALYTIC SUBUNIT). [SWISSPROT;Acc:Q08209]" PPP3CA 1.05458 0.268557151
0.283226 760 TUMOR ENDOTHELIAL MARKER 6; THYROID SPECIFIC PTB DOMAIN PROTEIN; TENSIN 3. [RefSeq;Acc:NM_022748] TNS3 1.0738 0.263760477
0.283289 990 HOMEOBOX PROTEIN ENGRAILED-2 (HU-EN-2). [SWISSPROT;Acc:P19622] EN2 1.11021 0.25516704
0.283453 1120 AGGF1 1.1302 0.250798974
0.283637 1063 PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-3 (HOMEOBOX PROTEIN PBX3). [SWISSPROT;Acc:P40426] PBX3 1.12271 0.252636032
0.284553 2765 ESTRADIOL 17 BETA-DEHYDROGENASE 4 (EC 1.1.1.62) (17-BETA-HSD 4) (17-BETA-HYDROXYSTEROID DEHYDROGENASE 4). [SWISSPROT;Acc:P51659] HSD17B4 1.40784 0.202120269
0.285075 1632 TRIPARTITE MOTIF PROTEIN 2. [SWISSPROT;Acc:Q9C040] TRIM2 1.19135 0.239287363
0.285122 1066 HOMEOBOX PROTEIN MEIS3 (MEIS1-RELATED PROTEIN 2) (FRAGMENT). [SWISSPROT;Acc:Q99687] MEIS3 1.12859 0.25263559
0.285611 1660 CYCLIN M4; ANCIENT CONSERVED DOMAIN PROTEIN 4. [RefSeq;Acc:NM_020184] CNNM4 1.19583 0.238839133
0.285613 73 TRANSCRIPTION FACTOR HES-1 (HAIRY AND ENHANCER OF SPLIT 1) (HAIRY- LIKE) (HHL) (HAIRY HOMOLOG). [SWISSPROT;Acc:Q14469] HES1 0.703261 0.406126602
0.286165 2215 PHOSPHOGLYCERATE KINASE 1 (EC 2.7.2.3) (PRIMER RECOGNITION PROTEIN 2) (PRP 2). [SWISSPROT;Acc:P00558] PGK1 1.2723 0.224919437
0.286436 2563 14-3-3 PROTEIN BETA/ALPHA (PROTEIN KINASE C INHIBITOR PROTEIN-1) (KCIP-1) (PROTEIN 1054). [SWISSPROT;Acc:P31946] YWHAB 1.34026 0.213716742
0.286606 2552 "DNA TOPOISOMERASE II, ALPHA ISOZYME (EC 5.99.1.3). [SWISSPROT;Acc:P11388]" no value 1.33628 0.214480498
0.287166 1204 KV CHANNEL INTERACTING PROTEIN 1; VESICLE APC-BINDING PROTEIN; A-TYPE POTASSIUM CHANNEL MODULATORY PROTEIN 1. [RefSeq;Acc:NM_014592] KCNIP1 1.15632 0.248344749
0.28719 1385 AUTOANTIGEN NGP-1. [SWISSPROT;Acc:Q13823] GNL2 1.17469 0.244481523
0.287772 1538 TRANSLATION INITIATION FACTOR EIF-2B DELTA SUBUNIT (EIF-2B GDP-GTP EXCHANGE FACTOR). [SWISSPROT;Acc:Q9UI10] EIF2B4 1.18956 0.241914658
0.287782 1498 HSGCN1 (FRAGMENT). [SPTREMBL;Acc:Q99736] GCN1L1 1.18538 0.242776156
0.287802 311 UBIQUITIN. [SWISSPROT;Acc:P02248] UBB 0.973671 0.295584443
0.288556 1241 C22orf25 1.16536 0.247611039
0.288835 957 CTP SYNTHASE (EC 6.3.4.2) (UTP--AMMONIA LIGASE) (CTP SYNTHETASE). [SWISSPROT;Acc:P17812] CTPS 1.12692 0.256304795
0.288916 359 "CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 5, 25 KD SUBUNIT; PRE-MRNA CLEAVAGE FACTOR IM (25KD); PRE-MRNA CLEAVAGE FACTOR IM, 25KD SUBUNIT. [RefSeq;Acc:NM_007006]" NUDT21 1.0267 0.281402552
0.289213 2242 DNA-DIRECTED RNA POLYMERASE I 16 KDA POLYPEPTIDE (EC 2.7.7.6) (RPA16). [SWISSPROT;Acc:Q9Y2S0] no value 1.29241 0.223778058
0.289435 933 ADENYLOSUCCINATE LYASE (EC 4.3.2.2) (ADENYLOSUCCINASE) (ASL) (ASASE). [SWISSPROT;Acc:P30566] ADSL 1.12698 0.256823546
0.289798 2411 TRANSCRIPTION FACTOR SMIF; DECAPPING ENZYME HDCP1A. [RefSeq;Acc:NM_018403] DCP1A 1.3266 0.218451681
0.290237 1334 AD24 PROTEIN. [RefSeq;Acc:NM_022451] NOC3L 1.18321 0.24529627
0.290469 133 GAMMA-AMINOBUTYRIC-ACID RECEPTOR GAMMA-3 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:Q99928] GABRG3 0.826637 0.351386401
134 INTERLEUKIN-1 RECEPTOR-ASSOCIATED KINASE 4; INTERLEUKIN-1 RECEPTOR ASSOCIATED KINASE 4. [RefSeq;Acc:NM_016123] no value
135 FORKHEAD BOX PROTEIN G1C (FORKHEAD-RELATED PROTEIN FKHL3) (HFK3) (FRAGMENT). [SWISSPROT;Acc:Q14488] FOXG1
136 PHOSPHATIDYLSERINE RECEPTOR; PHOSPHATIDYLSERINE RECEPTOR BETA. [RefSeq;Acc:NM_015167] JMJD6
0.29051 905 SIMILAR TO GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE (HYPOTHETICAL PROTEIN FLJ33258). [SPTREMBL;Acc:Q96EK6] GNPNAT1 1.12415 0.258426367
0.2912 2221 CYTOSOLIC NONSPECIFIC DIPEPTIDASE (GLUTAMATE CARBOXYPEPTIDASE-LIKE PROTEIN 1). [SWISSPROT;Acc:Q96KP4] CNDP2 1.29531 0.224811049
0.291311 1403 EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 2 (EUKARYOTIC TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT) (EIF-2-BETA). [SWISSPROT;Acc:P20042] EIF2S2 1.19358 0.244064914
0.291345 75 MITOCHONDRIAL RIBOSOME RECYCLING FACTOR. [RefSeq;Acc:NM_138777] MRRF 0.717375 0.406126503
0.292497 2239 "CASEIN KINASE I, DELTA ISOFORM (EC 2.7.1.-) (CKI-DELTA) (CKID). [SWISSPROT;Acc:P48730]" CSNK1D 1.30614 0.223940006
0.293026 3017 COATOMER DELTA SUBUNIT (DELTA-COAT PROTEIN) (DELTA-COP) (ARCHAIN). [SWISSPROT;Acc:P48444] ARCN1 2.41388 0.121392116

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/