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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description Gene Hugo measured Rank final expected
Results: HTML CSV LaTeX Showing element 651 to 700 of 3206 in total
description
Hugo
measured
Rank
final
expected
"GLYCOGEN PHOSPHORYLASE, BRAIN FORM (EC 2.4.1.1). [SWISSPROT;Acc:P11216]" PYGB 0.0231429 525 0.271903462 0.0851144
"GLYCOGEN PHOSPHORYLASE, LIVER FORM (EC 2.4.1.1). [SWISSPROT;Acc:P06737]" PYGL 0.0249116 527 0.271903112 0.0916194
"GLYCOGEN PHOSPHORYLASE, MUSCLE FORM (EC 2.4.1.1) (MYOPHOSPHORYLASE). [SWISSPROT;Acc:P11217]" PYGM 0.0229997 524 0.27190392 0.0845876
"GLYCOGEN [STARCH] SYNTHASE, LIVER (EC 2.4.1.11). [SWISSPROT;Acc:P54840]" GYS2 0.129726 3003 0.126288429 1.02722
"GLYCOGEN [STARCH] SYNTHASE, MUSCLE (EC 2.4.1.11). [SWISSPROT;Acc:P13807]" GYS1 0.158067 3005 0.12584852 1.25601
"GOLGI REASSEMBLY STACKING PROTEIN 2; GOLGI REASSEMBLY STACKING PROTEIN 2, 55 KDA. [RefSeq;Acc:NM_015530]" GORASP2 0.584026 2307 0.222083384 2.62976
"GRPE PROTEIN HOMOLOG 1, MITOCHONDRIAL PRECURSOR (MT-GRPE#1) (HMGE). [SWISSPROT;Acc:Q9HAV7]" GRPEL1 0.0851715 387 0.278747247 0.305551
"GRPE PROTEIN HOMOLOG 2, MITOCHONDRIAL PRECURSOR (MT-GRPE#2). [SWISSPROT;Acc:Q8TAA5]" GRPEL2 0.0678064 386 0.278747318 0.243254
"GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-1 SUBUNIT (ADENYLATE CYCLASE-INHIBITING G ALPHA PROTEIN). [SWISSPROT;Acc:P04898]" GNAI1 0.0510974 3060 0.105426545 0.484673
"GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-2 SUBUNIT (ADENYLATE CYCLASE-INHIBITING G ALPHA PROTEIN). [SWISSPROT;Acc:P04899]" GNAI2 0.0485629 3059 0.105432626 0.460606
"GUANINE NUCLEOTIDE-BINDING PROTEIN G(K), ALPHA SUBUNIT (G(I) ALPHA-3). [SWISSPROT;Acc:P08754]" GNAI3 0.0510974 3061 0.105426545 0.484673
"GUANINE NUCLEOTIDE-BINDING PROTEIN G(O), ALPHA SUBUNIT 1. [SWISSPROT;Acc:P09471]" GNAO1 0.299424 2931 0.158415339 1.89012
"GUANINE NUCLEOTIDE-BINDING PROTEIN G(Q), ALPHA SUBUNIT. [SWISSPROT;Acc:P50148]" GNAQ 0.0395834 3055 0.105460959 0.375337
"GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1 SUBUNIT (TRANSDUCIN ALPHA-1 CHAIN). [SWISSPROT;Acc:P11488]" GNAT1 0.044407 3057 0.105444244 0.421142
"GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-2 SUBUNIT (TRANSDUCIN ALPHA-2 CHAIN). [SWISSPROT;Acc:P19087]" GNAT2 0.0446932 3058 0.105443556 0.423859
"GUANINE NUCLEOTIDE-BINDING PROTEIN G(Y), ALPHA SUBUNIT (ALPHA-11). [SWISSPROT;Acc:P29992]" GNA11 0.0392019 3054 0.105462533 0.371714
"GUANINE NUCLEOTIDE-BINDING PROTEIN G(Z), ALPHA SUBUNIT (G(X) ALPHA CHAIN) (GZ-ALPHA). [SWISSPROT;Acc:P19086]" GNAZ 0.0438075 3056 0.10544641 0.415448
"HEXAPRENYLDIHYDROXYBENZOATE METHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.1.114) (DIHYDROXYHEXAPRENYLBENZOATE METHYLTRANSFERASE) (3,4- DIHYDROXY-5-HEXAPRENYLBENZOATE METHYLTRANSFERASE) (DHHB METHYLTRANSFERASE) (DHHB-MT) (DHHB-MTASE). [SWISSPRO" COQ3 0.0303966 1793 0.234838839 0.129436
"HIGH-MOBILITY GROUP 20B; SOX-LIKE TRANSCRIPTIONAL FACTOR; SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY E, MEMBER 1-RELATED. [RefSeq;Acc:NM_006339]" HMG20B 0.255373 322 0.288080184 0.886465
"HIGHLY EXPRESSED IN CANCER, RICH IN LEUCINE HEPTAD REPEATS. [RefSeq;Acc:NM_006101]" NDC80 0.0564981 1484 0.242929441 0.23257
"HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 1 (EC 2.1.1.43) (HISTONE H3-K9 METHYLTRANSFERASE 1) (H3-K9-HMTASE 1) (SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 1) (SU(VAR)3-9 HOMOLOG 1). [SWISSPROT;Acc:O43463]" SUV39H1 0.027437 2006 0.230689032 0.118935
"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]" SUV39H2 0.0323264 2008 0.230688646 0.14013
"HIV-1 TAT INTERACTIVE PROTEIN 2, 30KDA; TAT-INTERACTING PROTEIN (30KD); HIV-1 TAT INTERACTIVE PROTEIN 2, 30 KDA; HIV-1 TAT INTERACTIVE PROTEIN 2, 30 KD. [RefSeq;Acc:NM_006410]" HTATIP2 0.189189 2804 0.198284717 0.954128
"HOMER, NEURONAL IMMEDIATE EARLY GENE, 1B. [RefSeq;Acc:NM_004272]" HOMER1 0.137954 3078 0.099939871 1.38037
"HOMER, NEURONAL IMMEDIATE EARLY GENE, 2; HOMER HOMOLOG 3 (DROSOPHILA). [RefSeq;Acc:NM_004839]" HOMER2 0.174683 3083 0.099867935 1.74914
"HOMER, NEURONAL IMMEDIATE EARLY GENE, 3. [RefSeq;Acc:NM_004838]" HOMER3 0.13205 3077 0.099954583 1.3211
"HYDROXYACID OXIDASE 2 (EC 1.1.3.15) (HAOX2) ((S)-2-HYDROXY-ACID OXIDASE, PEROXISOMAL) (LONG CHAIN ALPHA-HYDROXY ACID OXIDASE) (LONG- CHAIN L-2-HYDROXY ACID OXIDASE). [SWISSPROT;Acc:Q9NYQ3]" HAO2 0.3063 2225 0.224548594 1.36407
"HYDROXYMETHYLGLUTARYL-COA SYNTHASE, CYTOPLASMIC (EC 2.3.3.10) (HMG-COA SYNTHASE) (3-HYDROXY-3-METHYLGLUTARYL COENZYME A SYNTHASE). [SWISSPROT;Acc:Q01581]" HMGCS1 0.0751775 2607 0.211948508 0.354697
"HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL PRECURSOR (EC 2.3.3.10) (HMG-COA SYNTHASE) (3-HYDROXY-3-METHYLGLUTARYL COENZYME A SYNTHASE). [SWISSPROT;Acc:P54868]" HMGCS2 0.0635814 2605 0.211948597 0.299985
"INHIBITOR OF GROWTH FAMILY, MEMBER 1-LIKE; INHIBITOR OF GROWTH 1-LIKE. [RefSeq;Acc:NM_001564]" ING2 0.132686 1546 0.241814878 0.548709
"INHIBITOR OF GROWTH FAMILY, MEMBER 1; INHIBITOR OF GROWTH 1. [RefSeq;Acc:NM_005537]" ING1 0.111297 1537 0.241959994 0.459981
"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]" INPP4A 0.0619579 100 0.373794298 0.165754
"INOSITOL POLYPHOSPHATE-4-PHOSPHATASE, TYPE II, 105KD; INOSITOL POLYPHOSPHATE 4-PHOSPHATASE II; 4-PHOSPHATASE II. [RefSeq;Acc:NM_003866]" INPP4B 0.046965 101 0.373794212 0.125644
"ISOCITRATE DEHYDROGENASE [NADP], MITOCHONDRIAL PRECURSOR (EC 1.1.1.42) (OXALOSUCCINATE DECARBOXYLASE) (IDH) (NADP+-SPECIFIC ICDH) (IDP) (ICD-M). [SWISSPROT;Acc:P48735]" IDH2 0.0716408 2853 0.191183864 0.374722
"ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT ALPHA, MITOCHONDRIAL PRECURSOR (EC 1.1.1.41) (ISOCITRIC DEHYDROGENASE) (NAD+-SPECIFIC ICDH). [SWISSPROT;Acc:P50213]" IDH3A 0.154876 2235 0.223997316 0.691419
"ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT BETA, MITOCHONDRIAL PRECURSOR (EC 1.1.1.41) (ISOCITRIC DEHYDROGENASE) (NAD+-SPECIFIC ICDH). [SWISSPROT;Acc:O43837]" IDH3B 0.0586323 2236 0.223996867 0.261755
"ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT GAMMA, MITOCHONDRIAL PRECURSOR (EC 1.1.1.41) (ISOCITRIC DEHYDROGENASE) (NAD+-SPECIFIC ICDH). [SWISSPROT;Acc:P51553]" IDH3G 0.0332619 2237 0.223996417 0.14849299999999999
"ISOLEUCYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.5) (ISOLEUCINE--TRNA LIGASE) (ILERS) (IRS). [SWISSPROT;Acc:P41252]" no value 0.0589414 1940 0.231616878 0.254478
"KARYOPHERIN BETA 2B, TRANSPORTIN; IMPORTIN 3. [RefSeq;Acc:NM_013433]" TNPO2 0.404881 532 0.271387971 1.49189
"KERATIN, ULTRA HIGH-SULFUR MATRIX PROTEIN A (UHS KERATIN A) (UHS KERA). [SWISSPROT;Acc:P26371]" no value 0.0250957 2530 0.214761155 0.116854
"KERATIN, ULTRA HIGH-SULFUR MATRIX PROTEIN B (UHS KERATIN B) (UHS KERB). [SWISSPROT;Acc:O75690]" KRTAP5-8 0.0249538 2535 0.214759798 0.116194
"KH DOMAIN CONTAINING, RNA BINDING, SIGNAL TRANSDUCTION ASSOCIATED 1; GAP-ASSOCIATED TYROSINE PHOSPHOPROTEIN P62 (SAM68). [RefSeq;Acc:NM_006559]" KHDRBS1 0.176025 150 0.351266675 0.501115
"KH DOMAIN CONTAINING, RNA BINDING, SIGNAL TRANSDUCTION ASSOCIATED 3; SAM68-LIKE PHOSPHOTYROSINE PROTEIN, T-STAR. [RefSeq;Acc:NM_006558]" KHDRBS3 0.230683 149 0.351266984 0.656717
"KH DOMAIN-CONTAINING, RNA-BINDING, SIGNAL TRANSDUCTION-ASSOCIATED PROTEIN 2; SAM68-LIKE MAMMALIAN PROTEIN 1. [RefSeq;Acc:NM_152688]" KHDRBS2 0.187708 151 0.351266433 0.534375
"LATS, LARGE TUMOR SUPPRESSOR, HOMOLOG 2; LATS (LARGE TUMOR SUPPRESSOR, DROSOPHILA) HOMOLOG 2. [RefSeq;Acc:NM_014572]" LATS2 0.0385424 553 0.270999768 0.142223
"LIM DOMAIN PROTEIN, CARDIAC (MUSCLE LIM PROTEIN) (CYSTEINE-RICH PROTEIN 3) (CRP3). [SWISSPROT;Acc:P50461]" CSRP3 0.101174 3116 0.088257513 1.14635
"LIPOAMIDE ACYLTRANSFERASE COMPONENT OF BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE COMPLEX, MITOCHONDRIAL PRECURSOR (EC 2.3.1.-) (E2) (DIHYDROLIPOAMIDE BRANCHED CHAIN TRANSACYLASE) (BCKAD E2 SUBUNIT). [SWISSPROT;Acc:P11182]" DBT 0.121426 1212 0.24805926 0.489504
"LIPOATE-PROTEIN LIGASE, MITOCHONDRIAL PRECURSOR (EC 6.-.-.-) (LIPOATE BIOSYNTHESIS PROTEIN) (LIPOYL LIGASE) (LIPOYLTRANSFERASE). [SWISSPROT;Acc:Q9Y234]" LIPT1 0.391899 2121 0.228122799 1.71793
"LIPOIC ACID SYNTHETASE, MITOCHONDRIAL (LIP-SYN) (LIPOATE SYNTHASE) (HUSSY-01) (FRAGMENT). [SWISSPROT;Acc:O43766]" LIAS 0.279023 2055 0.229714733 1.21465
"LIV-1 PROTEIN, ESTROGEN REGULATED. [RefSeq;Acc:NM_012319]" SLC39A6 0.0166846 1733 0.23703891 0.0703876

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/