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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expected Rank measured Gene description Hugo final
Results: HTML CSV LaTeX Showing element 2302 to 2351 of 3206 in total
expected
Rank
measured
description
Hugo
final
1.01213 3136 0.066175 MAGEB10 0.065381917
1.01314 494 0.277907 FUSED TOES HOMOLOG; LIKELY ORTHOLOG OF MOUSE FUSED TOES. [RefSeq;Acc:NM_022476] AKTIP 0.274302663
1.01339 3134 0.0662574 MELANOMA-ASSOCIATED ANTIGEN D1 (MAGE-D1 ANTIGEN) (NEUROTROPHIN RECEPTOR-INTERACTING MAGE HOMOLOG) (PRO2292). [SWISSPROT;Acc:Q9Y5V3] MAGED1 0.065381936
1.01402 3133 0.0662986 TROPHININ. [SWISSPROT;Acc:Q12816] TRO 0.065381945
1.015 99 0.380273 VAV-3 PROTEIN. [SWISSPROT;Acc:Q9UKW4] VAV3 0.374653202
1.01816 3185 0.0476371 CCDC104 0.04678744
1.01863 2378 0.223975 RIC8B 0.219878661
1.02096 3151 0.066752 MELANOMA-ASSOCIATED ANTIGEN B1 (MAGE-B1 ANTIGEN) (MAGE-XP ANTIGEN) (DSS-AHC CRITICAL INTERVAL MAGE SUPERFAMILY 10) (DAM10). [SWISSPROT;Acc:P43366] MAGEB4 0.065381602
1.02221 3028 0.121552 DOUBLE-STRAND BREAK REPAIR PROTEIN MRE11A (MRE11 HOMOLOG 1). [SWISSPROT;Acc:P49959] MRE11A 0.118910987
1.02341 2940 0.158961 CHROMOBOX PROTEIN HOMOLOG 3 (HETEROCHROMATIN PROTEIN 1 HOMOLOG GAMMA) (HP1 GAMMA) (MODIFIER 2 PROTEIN) (HECH). [SWISSPROT;Acc:Q13185] CBX3 0.155324845
1.02348 3140 0.0669169 MELANOMA-ASSOCIATED ANTIGEN D2 (MAGE-D2 ANTIGEN) (BREAST CANCER ASSOCIATED GENE 1 PROTEIN) (BCG-1) (11B6) (HEPATOCELLULAR CARCINOMA ASSOCIATED PROTEIN JCL-1). [SWISSPROT;Acc:Q9UNF1] MAGED2 0.065381737
1.02411 3138 0.0669581 HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN HCA1. [RefSeq;Acc:NM_020932] no value 0.065381746
1.02596 604 0.276018 HOMEOBOX PROTEIN OTX2. [SWISSPROT;Acc:P32243] OTX2 0.26903388
1.0262 501 0.281309 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 0.274126876
1.02669 2536 0.220469 ORNITHINE DECARBOXYLASE (EC 4.1.1.17) (ODC). [SWISSPROT;Acc:P11926] ODC1 0.214737652
1.0267 359 0.288916 "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 0.281402552
1.02722 3003 0.129726 "GLYCOGEN [STARCH] SYNTHASE, LIVER (EC 2.4.1.11). [SWISSPROT;Acc:P54840]" GYS2 0.126288429
1.02794 295 0.310048 EFHC2 0.301620717
1.02934 2922 0.172935 LAG1 LONGEVITY ASSURANCE HOMOLOG 2 ISOFORM 1; L3 PIGMENT; TUMOR METASTASIS-SUPPRESSOR. [RefSeq;Acc:NM_022075] LASS2 0.168005712
1.0307 2331 0.228054 40S RIBOSOMAL PROTEIN S27 (METALLOPAN-STIMULIN 1) (MPS-1). [SWISSPROT;Acc:P42677] no value 0.221261279
1.03319 930 0.266007 DYNEIN LIGHT CHAIN 2. [RefSeq;Acc:NM_080677] DYNLL2 0.257461841
1.03782 119 0.374769 NUCLEOLYSIN TIAR (TIA-1 RELATED PROTEIN). [SWISSPROT;Acc:Q01085] TIAL1 0.361111753
1.03785 1889 0.241532 DIHYDROFOLATE REDUCTASE (EC 1.5.1.3). [SWISSPROT;Acc:P00374] no value 0.232723419
1.0381 2172 0.235631 "ORNITHINE CARBAMOYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.3.3) (OTCASE) (ORNITHINE TRANSCARBAMYLASE). [SWISSPROT;Acc:P00480]" OTC 0.22698295
1.03901 615 0.279332 CALCIPRESSIN 3 (DOWN SYNDROME CANDIDATE REGION 1-LIKE PROTEIN 2) (MYOCYTE-ENRICHED CALCINEURIN INTERACTING PROTEIN 3) (MCIP3). [SWISSPROT;Acc:Q9UKA8] RCAN3 0.268844381
1.03903 274 0.316909 C14orf172 0.305004668
1.03955 3172 0.057781 NUCLEAR RNA EXPORT FACTOR 1 (TIP ASSOCIATING PROTEIN) (TIP-ASSOCIATED PROTEIN) (MRNA EXPORT FACTOR TAP). [SWISSPROT;Acc:Q9UBU9] NXF1 0.055582704
1.04017 1762 0.245894 RUVB-LIKE 2 (EC 3.6.1.-) (48-KDA TATA BOX-BINDING PROTEIN-INTERACTING PROTEIN) (48-KDA TBP-INTERACTING PROTEIN) (TIP49B) (REPRESSING PONTIN 52) (REPTIN 52) (51 KDA ERYTHROCYTE CYTOSOLIC PROTEIN) (ECP-51) (TIP60-ASSOCIATED PROTEIN 54-BETA) (TAP54-BETA) (CG RUVBL2 0.236397896
1.04189 1996 0.240428 "SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNIT, MITOCHONDRIAL PRECURSOR (INTEGRAL MEMBRANE PROTEIN CII-3) (QPS1) (QPS-1) (SUCCINATE DEHYDROGENASE COMPLEX SUBUNIT C) (SUCCINATE-UBIQUINONE OXIDOREDUCTASE CYTOCHROME B LARGE SUBUNIT) (CYBL). [SWISSPRO" SDHC 0.230761405
1.04193 2302 0.231616 DNA DIRECTED RNA POLYMERASE II POLYPEPTIDE J-RELATED GENE ISOFORM 3; RPB11B1ALPHA PROTEIN; RPB11B1BETA; DNA-DIRECTED RNA POLYMERASE II SUBUNIT 11. [RefSeq;Acc:NM_032959] no value 0.222295164
1.04237 2969 0.148933 COATOMER EPSILON SUBUNIT (EPSILON-COAT PROTEIN) (EPSILON-COP). [SWISSPROT;Acc:O14579] COPE 0.142879208
1.04353 94 0.394562 CBL E3 UBIQUITIN PROTEIN LIGASE (EC 6.3.2.-) (SIGNAL TRANSDUCTION PROTEIN CBL) (PROTO-ONCOGENE C-CBL). [SWISSPROT;Acc:P22681] CBL 0.378103169
1.04414 638 0.280063 "SPLICING FACTOR, ARGININE/SERINE-RICH 3 (PRE-MRNA SPLICING FACTOR SRP20) (X16 PROTEIN). [SWISSPROT;Acc:P23152]" SFRS3 0.26822361
1.04653 227 0.331603 KINESIN PROTEIN. [RefSeq;Acc:NM_032559] KIF2B 0.316859526
1.04775 612 0.281682 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 0.268844667
1.04777 3026 0.125021 BET3 HOMOLOG. [SWISSPROT;Acc:O43617] TRAPPC3 0.119321034
1.0479 2303 0.232938 DNA DIRECTED RNA POLYMERASE II POLYPEPTIDE J-RELATED GENE ISOFORM 1; RPB11B1ALPHA PROTEIN; RPB11B1BETA; DNA-DIRECTED RNA POLYMERASE II SUBUNIT 11. [RefSeq;Acc:NM_145325] no value 0.222290295
1.04802 1053 0.264806 CLATHRIN HEAVY CHAIN 1 (CLH-17). [SWISSPROT;Acc:Q00610] CLTC 0.252672659
1.0482 1803 0.24593 HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE; HUMAN GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE. [RefSeq;Acc:NM_004712] HGS 0.234621255
1.05097 2873 0.198456 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE BETA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 2) (1-AGPAT 2) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-BETA) (LPAAT-BETA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 2). [SWISSPROT;Acc:O15120] AGPAT2 0.18883127
1.05182 1123 0.263669 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 1 (26S PROTEASOME REGULATORY SUBUNIT S1) (26S PROTEASOME SUBUNIT P112). [SWISSPROT;Acc:Q99460] PSMD1 0.250678823
1.05366 3160 0.0681828 DJ756N5.1.1 (CONTINUES IN EM:AL133324 AS DJ1161H23.3) (FRAGMENT). [SPTREMBL;Acc:Q9H430] MYH7B 0.064710438
1.05445 2894 0.184777 "PYRUVATE KINASE, M1 ISOZYME (EC 2.7.1.40) (PYRUVATE KINASE MUSCLE ISOZYME) (CYTOSOLIC THYROID HORMONE-BINDING PROTEIN) (CTHBP) (THBP1). [SWISSPROT;Acc:P14618]" PKM2 0.175235431
1.05458 620 0.283215 "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 0.268557151
1.05643 126 0.375086 UBA/UBX 33.3 KDA PROTEIN. [SWISSPROT;Acc:Q04323] no value 0.3550505
1.0574 205 0.339248 TRANSCRIPTION FACTOR JUN-B. [SWISSPROT;Acc:P17275] JUNB 0.32083223
1.06471 2427 0.231972 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 (EC 2.7.1.-) (TRANSFORMING GROWTH FACTOR-BETA-ACTIVATED KINASE 1) (TGF-BETA- ACTIVATED KINASE 1). [SWISSPROT;Acc:O43318] MAP3K7 0.217873412
1.06498 790 0.279039 SYNTAXIN 16 (SYN16). [SWISSPROT;Acc:O14662] STX16 0.262013371
1.06655 335 0.304036 MYC PROTO-ONCOGENE PROTEIN (C-MYC). [SWISSPROT;Acc:P01106] MYC 0.285064929
1.06742 816 0.278946 ETHANOLAMINE-PHOSPHATE CYTIDYLYLTRANSFERASE (EC 2.7.7.14) (PHOSPHORYLETHANOLAMINE TRANSFERASE) (CTP:PHOSPHOETHANOLAMINE CYTIDYLYLTRANSFERASE). [SWISSPROT;Acc:Q99447] PCYT2 0.261327313

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/