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 Gene Rank description measured final Hugo
Results: HTML CSV LaTeX Showing element 2402 to 2451 of 3206 in total
expected
Rank
description
measured
final
Hugo
1.12425 1831 0.263169 0.234084056 TSR1
1.125 3162 "MYOSIN HEAVY CHAIN, FAST SKELETAL MUSCLE, EMBRYONIC (MUSCLE EMBRYONIC MYOSIN HEAVY CHAIN) (SMHCE). [SWISSPROT;Acc:P11055]" 0.0727992 0.0647104 MYH3
1.12566 2678 UDP-GLUCOSE 4-EPIMERASE (EC 5.1.3.2) (GALACTOWALDENASE) (UDP- GALACTOSE 4-EPIMERASE). [SWISSPROT;Acc:Q14376] 0.234953 0.208724659 GALE
1.12603 1142 "TUMOR NECROSIS FACTOR, ALPHA-INDUCED PROTEIN 1, ENDOTHELIAL (B12 PROTEIN). [SWISSPROT;Acc:Q13829]" 0.281828 0.250284628 TNFAIP1
1.12692 957 CTP SYNTHASE (EC 6.3.4.2) (UTP--AMMONIA LIGASE) (CTP SYNTHETASE). [SWISSPROT;Acc:P17812] 0.288835 0.256304795 CTPS
1.12698 933 ADENYLOSUCCINATE LYASE (EC 4.3.2.2) (ADENYLOSUCCINASE) (ASL) (ASASE). [SWISSPROT;Acc:P30566] 0.289435 0.256823546 ADSL
1.12859 1066 HOMEOBOX PROTEIN MEIS3 (MEIS1-RELATED PROTEIN 2) (FRAGMENT). [SWISSPROT;Acc:Q99687] 0.285122 0.25263559 MEIS3
1.12934 495 R3H DOMAIN PROTEIN 1. [SWISSPROT;Acc:Q15032] 0.309779 0.274300919 R3HDM1
1.1302 1120 0.283453 0.250798974 AGGF1
1.13453 2181 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 6 (PAK-INTERACTING EXCHANGE FACTOR ALPHA) (ALPHA-PIX) (COOL-2). [SWISSPROT;Acc:Q15052] 0.257131 0.226640988 ARHGEF6
1.13458 1239 "POTASSIUM VOLTAGE-GATED CHANNEL, SHAL-RELATED SUBFAMILY, MEMBER 1; SHAL-TYPE POTASSIUM CHANNEL; VOLTAGE-GATED POTASSIUM CHANNEL KV4.1. [RefSeq;Acc:NM_004979]" 0.280939 0.247614976 KCND1
1.13756 1716 VACUOLAR PROTON TRANSLOCATING ATPASE 116 KDA SUBUNIT A ISOFORM 1 (CLATHRIN-COATED VESICLE/SYNAPTIC VESICLE PROTON PUMP 116 KDA SUBUNIT) (VACUOLAR PROTON PUMP SUBUNIT 1) (VACUOLAR ADENOSINE TRIPHOSPHATASE SUBUNIT AC116). [SWISSPROT;Acc:Q93050] 0.269961 0.237315834 ATP6V0A1
1.13816 1658 TRIPARTITE MOTIF PROTEIN 3 (RING FINGER PROTEIN 22) (BRAIN-EXPRESSED RING FINGER PROTEIN). [SWISSPROT;Acc:O75382] 0.271838 0.238839882 TRIM3
1.13826 3165 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, FETAL (MYOSIN HEAVY CHAIN IIB) (MYHC-IIB). [SWISSPROT;Acc:Q9Y623]" 0.0736571 0.06471026 MYH4
1.13857 3159 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, PERINATAL (MYHC-PERINATAL). [SWISSPROT;Acc:P13535]" 0.0736775 0.064710558 MYH8
1.13895 246 "5'-AMP-ACTIVATED PROTEIN KINASE, BETA-1 SUBUNIT (AMPK BETA-1 CHAIN) (AMPKB). [SWISSPROT;Acc:Q9Y478]" 0.355846 0.312433382 PRKAB1
1.13987 528 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 12B ISOFORM A; MYOSIN PHOSPHATASE REGULATORY SUBUNIT; MYOSIN PHOSPHATASE, TARGET SUBUNIT 2. [RefSeq;Acc:NM_002481]" 0.309836 0.271816962 PPP1R12B
1.14212 599 ZINC FINGER PROTEIN ZIC 2 (ZINC FINGER PROTEIN OF THE CEREBELLUM 2). [SWISSPROT;Acc:O95409] 0.307359 0.269112703 ZIC2
1.14255 1238 TBP-ASSOCIATED FACTOR 172 (TAF-172) (TAF(II)170). [SWISSPROT;Acc:O14981] 0.283008 0.247698569 BTAF1
1.14298 2306 0.25396 0.222191114 no value
1.14316 753 LUPUS LA PROTEIN (SJOGREN SYNDROME TYPE B ANTIGEN) (SS-B) (LA RIBONUCLEOPROTEIN) (LA AUTOANTIGEN). [SWISSPROT;Acc:P05455] 0.302351 0.264487036 SSB
1.14331 3164 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, ADULT 2 (MYOSIN HEAVY CHAIN IIA) (MYHC-IIA). [SWISSPROT;Acc:Q9UKX2]" 0.0739839 0.064710271 MYH2
1.14341 1612 "UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2; 1 ALPHA,25-DIHYDROXYVITAMIN D3-INDUCIBLE; ENTEROCYTE DIFFERENTIATION PROMOTING FACTOR; METHYL METHANESULFONATE SENSITIVE 2, S. CEREVISIAE, HOMOLOG OF. [RefSeq;Acc:NM_003350]" 0.274194 0.239803745 UBE2V2
1.14368 1329 PROBABLE ATP-DEPENDENT 61 KDA NUCLEOLAR RNA HELICASE (DEAD-BOX PROTEIN 21). [SWISSPROT;Acc:Q9NY93] 0.280718 0.245451525 DDX56
1.14373 2243 ARGININOSUCCINATE LYASE (EC 4.3.2.1) (ARGINOSUCCINASE) (ASAL). [SWISSPROT;Acc:P04424] 0.255929 0.223766973 ASL
1.14583 3158 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, ADULT 1 (MYOSIN HEAVY CHAIN IIX/D) (MYHC-IIX/D). [SWISSPROT;Acc:P12882]" 0.0741473 0.064710559 MYH1
1.14635 3116 "LIM DOMAIN PROTEIN, CARDIAC (MUSCLE LIM PROTEIN) (CYSTEINE-RICH PROTEIN 3) (CRP3). [SWISSPROT;Acc:P50461]" 0.101174 0.088257513 CSRP3
1.147 104 FLAVOPROTEIN OXIDOREDUCTASE MICAL2. [RefSeq;Acc:NM_014632] 0.42874 0.373792502 MICAL2
1.14705 1597 PUTATIVE EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT (EIF-3) (FRAGMENT). [SWISSPROT;Acc:O75153] 0.275535 0.240211848 KIAA0664
1.14976 500 ABL-INTERACTOR 2; ABL-INTERACTING PROTEIN 1 (SH3-CONTAINING PROTEIN); ABL BINDING PROTEIN 3; ARG PROTEIN TYROSINE KINASE-BINDING PROTEIN; ABL-INTERACTOR PROTEIN 2B; SIMILAR TO SPECTRIN SH3 DOMAIN BINDING PROTEIN 1. [RefSeq;Acc:NM_005759] 0.315262 0.274198094 ABI2
1.15171 517 0.313715 0.272390619 UBAP2L
1.15298 2898 G2/MITOTIC-SPECIFIC CYCLIN B2. [SWISSPROT;Acc:O95067] 0.201803 0.175027321 CCNB2
1.15632 1204 KV CHANNEL INTERACTING PROTEIN 1; VESICLE APC-BINDING PROTEIN; A-TYPE POTASSIUM CHANNEL MODULATORY PROTEIN 1. [RefSeq;Acc:NM_014592] 0.287166 0.248344749 KCNIP1
1.15814 2337 0.256113 0.221141658 D2HGDH
1.15907 2232 APOPTOSIS-INDUCING FACTOR (AIF)-HOMOLOGOUS MITOCHONDRION-ASSOCIATED INDUCER OF DEATH; P53-RESPONSIVE GENE 3. [RefSeq;Acc:NM_032797] 0.259882 0.224215966 AIFM2
1.15996 2479 PRE-MRNA CLEAVAGE COMPLEX II PROTEIN PCF11 (FRAGMENT). [SWISSPROT;Acc:O94913] 0.251152 0.216517811 PCF11
1.16002 160 HUNTINGTIN-INTERACTING PROTEIN HYPA/FBP11 (FRAGMENT). [SPTREMBL;Acc:O75404] 0.40616 0.350131894 no value
1.16068 1047 SOLUBLE LIVER ANTIGEN/LIVER PANCREAS ANTIGEN. [RefSeq;Acc:NM_153825] 0.293391 0.252775097 SEPSECS
1.1607 1937 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM7. [SWISSPROT;Acc:Q9UK45] 0.268923 0.231690359 no value
1.16185 2554 "DNA TOPOISOMERASE II, BETA ISOZYME (EC 5.99.1.3). [SWISSPROT;Acc:Q02880]" 0.249175 0.214464001 TOP2B
1.16362 2571 SODIUM-DEPENDENT MULTIVITAMIN TRANSPORTER (NA(+)-DEPENDENT MULTIVITAMIN TRANSPORTER). [SWISSPROT;Acc:Q9Y289] 0.248255 0.213347141 SLC5A6
1.16418 1780 ADENINE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.7) (APRT). [SWISSPROT;Acc:P07741] 0.273997 0.235356216 no value
1.1643 2816 ZINC FINGER PROTEIN 444; ENDOTHELIAL ZINC FINGER PROTEIN 2. [RefSeq;Acc:NM_018337] 0.225841 0.193971485 ZNF444
1.16536 1241 0.288556 0.247611039 C22orf25
1.16562 1590 EVOLUTIONARILY CONSERVED SIGNALING INTERMEDIATE IN TOLL PATHWAY; ECSIT. [RefSeq;Acc:NM_016581] 0.28028 0.240455723 ECSIT
1.16629 1061 PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-2 (HOMEOBOX PROTEIN PBX2) (G17 PROTEIN). [SWISSPROT;Acc:P40425] 0.294647 0.252636137 no value
1.16696 105 VAV-2 PROTEIN. [SWISSPROT;Acc:P52735] 0.433722 0.371668266 VAV2
1.1674 2 RAD50-INTERACTING PROTEIN 1. [RefSeq;Acc:NM_021930] 1.28125 1.097524413 RINT1
3 RHO-RELATED BTB DOMAIN-CONTAINING PROTEIN 2 (DELETED IN BREAST CANCER 2 GENE PROTEIN) (P83). [SWISSPROT;Acc:Q9BYZ6] RHOBTB2
1.17469 1385 AUTOANTIGEN NGP-1. [SWISSPROT;Acc:Q13823] 0.28719 0.244481523 GNL2

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/