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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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 2758 to 2807 of 3206 in total
Rank
description
measured
expected
final
Hugo
2758 0.0721926 0.356265 0.202637363 SAPS2
2759 SPORULATION-INDUCED TRANSCRIPT 4-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_018312] 0.0957295 0.472418 0.202637283 SAPS3
2760 SERINE/THREONINE PROTEIN PHOSPHATASE 6 (EC 3.1.3.16) (PP6). [SWISSPROT;Acc:O00743] 0.0987657 0.487402 0.202637043 PPP6C
2761 0.0657247 0.324347 0.202636991 SAPS1
2762 ACETYL-COA CARBOXYLASE 2 (EC 6.4.1.2) (ACC-BETA) [INCLUDES: BIOTIN CARBOXYLASE (EC 6.3.4.14)]. [SWISSPROT;Acc:O00763] 0.938896 4.63429 0.202597593 ACACB
2763 SKELETAL MUSCLE LIM-PROTEIN 2 (SLIM 2) (FOUR AND A HALF LIM DOMAINS PROTEIN 3) (FHL-3). [SWISSPROT;Acc:Q13643] 0.669714 3.30667 0.202534272 FHL3
2764 SKELETAL MUSCLE LIM-PROTEIN 3 (SLIM 3) (LIM-DOMAIN PROTEIN DRAL) (FOUR AND A HALF LIM DOMAINS PROTEIN 2) (FHL-2). [SWISSPROT;Acc:Q14192] 0.682678 3.37289 0.202401501 FHL2
2765 ESTRADIOL 17 BETA-DEHYDROGENASE 4 (EC 1.1.1.62) (17-BETA-HSD 4) (17-BETA-HYDROXYSTEROID DEHYDROGENASE 4). [SWISSPROT;Acc:P51659] 0.284553 1.40784 0.202120269 HSD17B4
2766 DEAD/H (ASP-GLU-ALA-ASP/HIS) BOX POLYPEPTIDE 11; DEAD/H BOX-11 (CHL1-RELATED HELICASE GENE-1); YEAST CHL1 HOMOLOG. [RefSeq;Acc:NM_030655] 0.339171 1.6782 0.20210404 DDX12
2767 HELICASE (FRAGMENT). [SPTREMBL;Acc:Q92771] 0.324046 1.60341 0.202098029 no value
2768 ZINC FINGER PROTEIN 277. [SWISSPROT;Acc:Q9NRM2] 0.0570468 0.282946 0.20161727
2769 SIMILAR TO ZINC FINGER PROTEIN 277. [SPTREMBL;Acc:Q8WWA6] 0.0486609 0.241353 0.201617133
2770 LACTOYLGLUTATHIONE LYASE (EC 4.4.1.5) (METHYLGLYOXALASE) (ALDOKETOMUTASE) (GLYOXALASE I) (GLX I) (KETONE-ALDEHYDE MUTASE) (S-D-LACTOYLGLUTATHIONE METHYLGLYOXAL LYASE). [SWISSPROT;Acc:Q04760] 0.570693 2.83362 0.201400682 GLO1
2771 MAWD BINDING PROTEIN (UNKNOWN PROTEIN 32 FROM 2D-PAGE OF LIVER TISSUE). [SWISSPROT;Acc:P30039] 0.0230825 0.11461 0.201400401 PBLD
2772 LYSOPHOSPHOLIPASE I; LYSOPHOSPHOLIPASE 1; LYSOPHOSPHOLIPID-SPECIFIC LYSOPHOSPHOLIPASE; ACYL-PROTEIN THIOESTERASE-1. [RefSeq;Acc:NM_006330] LYPLA1
2773 DJ570F3.6 (NOVEL PROTEIN SIMILAR TO LYSOPHOSPHOLIPASE II (LYPLA2)). [SPTREMBL;Acc:Q9UGE0] 0.0202703 0.100647 0.201399942 no value
2774 LYSOPHOSPHOLIPASE II; ACYL-PROTEIN THIOESTERASE. [RefSeq;Acc:NM_007260] 0.0206348 0.102457 0.201399612 LYPLA2P1
2775 ORPHAN NUCLEAR RECEPTOR NURR1 (IMMEDIATE-EARLY RESPONSE PROTEIN NOT) (TRANSCRIPTIONALLY INDUCIBLE NUCLEAR RECEPTOR). [SWISSPROT;Acc:P43354] 0.603026 2.99447 0.201379877 NR4A2
2776 NUCLEAR HORMONE RECEPTOR NOR-1 (NEURON-DERIVED ORPHAN RECEPTOR 1) (MITOGEN INDUCED NUCLEAR ORPHAN RECEPTOR). [SWISSPROT;Acc:Q92570] 0.515632 2.56143 0.201306302 NR4A3
2777 ORPHAN NUCLEAR RECEPTOR HMR (EARLY RESPONSE PROTEIN NAK1) (TR3 ORPHAN RECEPTOR). [SWISSPROT;Acc:P22736] 0.508993 2.52853 0.201299965 NR4A1
2778 "ELECTRON TRANSFER FLAVOPROTEIN ALPHA-SUBUNIT, MITOCHONDRIAL PRECURSOR (ALPHA-ETF). [SWISSPROT;Acc:P13804]" 0.396527 1.97038 0.201243922 ETFA
2779 INSULIN GENE ENHANCER PROTEIN ISL-2 (ISLET-2). [SWISSPROT;Acc:Q96A47] 0.369521 1.8374 0.201110809 ISL2
2780 0.179735 0.894194 0.201002243 TARSL2
2781 PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN (EC 6.1.1.20) (PHENYLALANINE-- TRNA LIGASE BETA CHAIN) (PHERS) (HSPC173). [SWISSPROT;Acc:Q9NSD9] 0.0470468 0.234118 0.200953365 FARSB
2782 SYNAPTOTAGMIN XII (SYTXII). [SWISSPROT;Acc:Q8IV01] 0.236204 1.17564 0.200915246 SYT12
2783 CA2+-DEPENDENT ENDOPLASMIC RETICULUM NUCLEOSIDE DIPHOSPHATASE; APYRASE; SOLUBLE CALCIUM-ACTIVATED NUCLEOTIDASE SCAN-1. [RefSeq;Acc:NM_138793] 0.116337 0.580323 0.200469394 CANT1
2784 0.469598 2.34488 0.200265259 FAHD1
2785 WD REPEAT AND FYVE DOMAIN CONTAINING 1 ISOFORM 1; PHOSPHOINOSITIDE-BINDING PROTEIN SR1; WD40 AND FYVE DOMAIN CONTAINING 1. [RefSeq;Acc:NM_020830] 0.447508 2.23848 0.199916014 WDFY1
2786 PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN (EC 6.1.1.20) (PHENYLALANINE- -TRNA LIGASE ALPHA CHAIN) (PHERS) (CML33). [SWISSPROT;Acc:Q9Y285] 0.0790566 0.39545 0.199915539 FARSA
2787 PHENYLALANINE-TRNA SYNTHETASE. [RefSeq;Acc:NM_006567] FARS2
2788 POLYPOSIS LOCUS PROTEIN 1 (TB2 PROTEIN). [SWISSPROT;Acc:Q00765] 0.195503 0.977987 0.199903475 REEP5
2789 0.0519078 0.259665 0.199902952 LYCAT
2790 POLYPOSIS LOCUS PROTEIN 1-LIKE 1; LIKELY ORTHOLOG OF MOUSE POLYPOSIS LOCUS PROTEIN 1-LIKE 1. [RefSeq;Acc:NM_138393] 0.150538 0.753056 0.199902796 REEP6
2791 TRAP/MEDIATOR COMPLEX COMPONENT TRAP25. [RefSeq;Acc:NM_080651] 0.0557223 0.278747 0.199902779 MED30
2792 0.0536744 0.268503 0.199902422 WDR32
2793 STROMAL INTERACTION MOLECULE 1 PRECURSOR. [SWISSPROT;Acc:Q13586] 0.0623579 0.311942 0.199902225 STIM1
2794 "ACYL-COA DEHYDROGENASE, MEDIUM-CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.3) (MCAD). [SWISSPROT;Acc:P11310]" ACADM
2795 SERINE/THREONINE-PROTEIN KINASE PAK 4 (EC 2.7.1.-) (P21-ACTIVATED KINASE 4) (PAK-4). [SWISSPROT;Acc:O96013] 0.145818 0.729447 0.199902118 PAK4
2796 SERINE/THREONINE-PROTEIN KINASE PAK 7 (EC 2.7.1.-) (P21-ACTIVATED KINASE 7) (PAK-7) (PAK-5). [SWISSPROT;Acc:Q9P286] 0.193542 0.968184 0.199902085 PAK7
2797 STROMAL INTERACTION MOLECULE 2 PRECURSOR. [SWISSPROT;Acc:Q9P246] 0.0487701 0.24397 0.199902037 STIM2
2798 WD REPEAT- AND FYVE DOMAIN-CONTAINING PROTEIN 2; WD40 AND FYVE DOMAIN CONTAINING 2. [RefSeq;Acc:NM_052950] 0.533046 2.66667 0.199892 WDFY2
2799 "ATAXIN 2; OLIVOPONTOCEREBELLAR ATAXIA 2, AUTOSOMAL DOMINANT. [RefSeq;Acc:NM_002973]" 0.0572133 0.287777 0.198811232 no value
2800 ATAXIN 2 RELATED PROTEIN ISOFORM A; ATAXIN-2 DOMAIN PROTEIN. [RefSeq;Acc:NM_007245] 0.070265 0.353426 0.198811067 ATXN2L
2801 TUMOR PROTEIN D53 (HD53) (D52-LIKE 1). [SWISSPROT;Acc:Q16890] 0.142496 0.71709 0.198714248 TPD52L1
2802 TUMOR PROTEIN D52 (N8 PROTEIN). [SWISSPROT;Acc:P55327] 0.169565 0.853344 0.198706501 TPD52
2803 MULTISYNTHETASE COMPLEX AUXILIARY COMPONENT P43 [CONTAINS: ENDOTHELIAL-MONOCYTE ACTIVATING POLYPEPTIDE II (EMAP-II) (SMALL INDUCIBLE CYTOKINE SUBFAMILY E MEMBER 1)]. [SWISSPROT;Acc:Q12904] 0.388823 1.9597 0.19840945 SCYE1
2804 "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]" 0.189189 0.954128 0.198284717 HTATIP2
2805 KRUPPEL-RELATED ZINC FINGER PROTEIN HCKROX. [RefSeq;Acc:NM_015872] 0.0949294 0.480144 0.19771027 ZBTB7B
2806 ZINC FINGER PROTEIN 288 (DENDRITIC-DERIVED BTB/POZ ZINC FINGER PROTEIN). [SWISSPROT;Acc:Q9HC78] 0.101567 0.513743 0.197700017 ZBTB20
2807 0.101691 0.514373 0.197698946 no value

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/