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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final expected Gene measured Rank description Hugo
Results: HTML CSV LaTeX Showing element 402 to 451 of 3206 in total
final
expected
measured
Rank
description
Hugo
0.19771027 0.480144 0.0949294 2805 KRUPPEL-RELATED ZINC FINGER PROTEIN HCKROX. [RefSeq;Acc:NM_015872] ZBTB7B
0.198284717 0.954128 0.189189 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]" HTATIP2
0.19840945 1.9597 0.388823 2803 MULTISYNTHETASE COMPLEX AUXILIARY COMPONENT P43 [CONTAINS: ENDOTHELIAL-MONOCYTE ACTIVATING POLYPEPTIDE II (EMAP-II) (SMALL INDUCIBLE CYTOKINE SUBFAMILY E MEMBER 1)]. [SWISSPROT;Acc:Q12904] SCYE1
0.198706501 0.853344 0.169565 2802 TUMOR PROTEIN D52 (N8 PROTEIN). [SWISSPROT;Acc:P55327] TPD52
0.198714248 0.71709 0.142496 2801 TUMOR PROTEIN D53 (HD53) (D52-LIKE 1). [SWISSPROT;Acc:Q16890] TPD52L1
0.198811067 0.353426 0.070265 2800 ATAXIN 2 RELATED PROTEIN ISOFORM A; ATAXIN-2 DOMAIN PROTEIN. [RefSeq;Acc:NM_007245] ATXN2L
0.198811232 0.287777 0.0572133 2799 "ATAXIN 2; OLIVOPONTOCEREBELLAR ATAXIA 2, AUTOSOMAL DOMINANT. [RefSeq;Acc:NM_002973]" no value
0.199892 2.66667 0.533046 2798 WD REPEAT- AND FYVE DOMAIN-CONTAINING PROTEIN 2; WD40 AND FYVE DOMAIN CONTAINING 2. [RefSeq;Acc:NM_052950] WDFY2
0.199902037 0.24397 0.0487701 2797 STROMAL INTERACTION MOLECULE 2 PRECURSOR. [SWISSPROT;Acc:Q9P246] STIM2
0.199902085 0.968184 0.193542 2796 SERINE/THREONINE-PROTEIN KINASE PAK 7 (EC 2.7.1.-) (P21-ACTIVATED KINASE 7) (PAK-7) (PAK-5). [SWISSPROT;Acc:Q9P286] PAK7
0.199902118 0.729447 0.145818 2795 SERINE/THREONINE-PROTEIN KINASE PAK 4 (EC 2.7.1.-) (P21-ACTIVATED KINASE 4) (PAK-4). [SWISSPROT;Acc:O96013] PAK4
0.199902225 0.311942 0.0623579 2793 STROMAL INTERACTION MOLECULE 1 PRECURSOR. [SWISSPROT;Acc:Q13586] STIM1
2794 "ACYL-COA DEHYDROGENASE, MEDIUM-CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.3) (MCAD). [SWISSPROT;Acc:P11310]" ACADM
0.199902422 0.268503 0.0536744 2792 WDR32
0.199902779 0.278747 0.0557223 2791 TRAP/MEDIATOR COMPLEX COMPONENT TRAP25. [RefSeq;Acc:NM_080651] MED30
0.199902796 0.753056 0.150538 2790 POLYPOSIS LOCUS PROTEIN 1-LIKE 1; LIKELY ORTHOLOG OF MOUSE POLYPOSIS LOCUS PROTEIN 1-LIKE 1. [RefSeq;Acc:NM_138393] REEP6
0.199902952 0.259665 0.0519078 2789 LYCAT
0.199903475 0.977987 0.195503 2788 POLYPOSIS LOCUS PROTEIN 1 (TB2 PROTEIN). [SWISSPROT;Acc:Q00765] REEP5
0.199915539 0.39545 0.0790566 2786 PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN (EC 6.1.1.20) (PHENYLALANINE- -TRNA LIGASE ALPHA CHAIN) (PHERS) (CML33). [SWISSPROT;Acc:Q9Y285] FARSA
2787 PHENYLALANINE-TRNA SYNTHETASE. [RefSeq;Acc:NM_006567] FARS2
0.199916014 2.23848 0.447508 2785 WD REPEAT AND FYVE DOMAIN CONTAINING 1 ISOFORM 1; PHOSPHOINOSITIDE-BINDING PROTEIN SR1; WD40 AND FYVE DOMAIN CONTAINING 1. [RefSeq;Acc:NM_020830] WDFY1
0.200265259 2.34488 0.469598 2784 FAHD1
0.200469394 0.580323 0.116337 2783 CA2+-DEPENDENT ENDOPLASMIC RETICULUM NUCLEOSIDE DIPHOSPHATASE; APYRASE; SOLUBLE CALCIUM-ACTIVATED NUCLEOTIDASE SCAN-1. [RefSeq;Acc:NM_138793] CANT1
0.200915246 1.17564 0.236204 2782 SYNAPTOTAGMIN XII (SYTXII). [SWISSPROT;Acc:Q8IV01] SYT12
0.200953365 0.234118 0.0470468 2781 PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN (EC 6.1.1.20) (PHENYLALANINE-- TRNA LIGASE BETA CHAIN) (PHERS) (HSPC173). [SWISSPROT;Acc:Q9NSD9] FARSB
0.201002243 0.894194 0.179735 2780 TARSL2
0.201110809 1.8374 0.369521 2779 INSULIN GENE ENHANCER PROTEIN ISL-2 (ISLET-2). [SWISSPROT;Acc:Q96A47] ISL2
0.201243922 1.97038 0.396527 2778 "ELECTRON TRANSFER FLAVOPROTEIN ALPHA-SUBUNIT, MITOCHONDRIAL PRECURSOR (ALPHA-ETF). [SWISSPROT;Acc:P13804]" ETFA
0.201299965 2.52853 0.508993 2777 ORPHAN NUCLEAR RECEPTOR HMR (EARLY RESPONSE PROTEIN NAK1) (TR3 ORPHAN RECEPTOR). [SWISSPROT;Acc:P22736] NR4A1
0.201306302 2.56143 0.515632 2776 NUCLEAR HORMONE RECEPTOR NOR-1 (NEURON-DERIVED ORPHAN RECEPTOR 1) (MITOGEN INDUCED NUCLEAR ORPHAN RECEPTOR). [SWISSPROT;Acc:Q92570] NR4A3
0.201379877 2.99447 0.603026 2775 ORPHAN NUCLEAR RECEPTOR NURR1 (IMMEDIATE-EARLY RESPONSE PROTEIN NOT) (TRANSCRIPTIONALLY INDUCIBLE NUCLEAR RECEPTOR). [SWISSPROT;Acc:P43354] NR4A2
0.201399612 0.102457 0.0206348 2774 LYSOPHOSPHOLIPASE II; ACYL-PROTEIN THIOESTERASE. [RefSeq;Acc:NM_007260] LYPLA2P1
0.201399942 0.100647 0.0202703 2773 DJ570F3.6 (NOVEL PROTEIN SIMILAR TO LYSOPHOSPHOLIPASE II (LYPLA2)). [SPTREMBL;Acc:Q9UGE0] no value
0.201400401 0.11461 0.0230825 2771 MAWD BINDING PROTEIN (UNKNOWN PROTEIN 32 FROM 2D-PAGE OF LIVER TISSUE). [SWISSPROT;Acc:P30039] PBLD
2772 LYSOPHOSPHOLIPASE I; LYSOPHOSPHOLIPASE 1; LYSOPHOSPHOLIPID-SPECIFIC LYSOPHOSPHOLIPASE; ACYL-PROTEIN THIOESTERASE-1. [RefSeq;Acc:NM_006330] LYPLA1
0.201400682 2.83362 0.570693 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] GLO1
0.201617133 0.241353 0.0486609 2769 SIMILAR TO ZINC FINGER PROTEIN 277. [SPTREMBL;Acc:Q8WWA6] no value
0.20161727 0.282946 0.0570468 2768 ZINC FINGER PROTEIN 277. [SWISSPROT;Acc:Q9NRM2]
0.202098029 1.60341 0.324046 2767 HELICASE (FRAGMENT). [SPTREMBL;Acc:Q92771]
0.20210404 1.6782 0.339171 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] DDX12
0.202120269 1.40784 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
0.202401501 3.37289 0.682678 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] FHL2
0.202534272 3.30667 0.669714 2763 SKELETAL MUSCLE LIM-PROTEIN 2 (SLIM 2) (FOUR AND A HALF LIM DOMAINS PROTEIN 3) (FHL-3). [SWISSPROT;Acc:Q13643] FHL3
0.202597593 4.63429 0.938896 2762 ACETYL-COA CARBOXYLASE 2 (EC 6.4.1.2) (ACC-BETA) [INCLUDES: BIOTIN CARBOXYLASE (EC 6.3.4.14)]. [SWISSPROT;Acc:O00763] ACACB
0.202636991 0.324347 0.0657247 2761 SAPS1
0.202637043 0.487402 0.0987657 2760 SERINE/THREONINE PROTEIN PHOSPHATASE 6 (EC 3.1.3.16) (PP6). [SWISSPROT;Acc:O00743] PPP6C
0.202637283 0.472418 0.0957295 2759 SPORULATION-INDUCED TRANSCRIPT 4-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_018312] SAPS3
0.202637363 0.356265 0.0721926 2758 SAPS2
0.202672931 5.26987 1.06806 2757 ACETYL-COA CARBOXYLASE 1 (EC 6.4.1.2) (ACC-ALPHA) [INCLUDES: BIOTIN CARBOXYLASE (EC 6.3.4.14)]. [SWISSPROT;Acc:Q13085] ACACA
0.202699899 0.756695 0.153382 2756 ATAD1

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/