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 Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3008 to 3057 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
752 step ii splicing factor slu7. [refseq;acc:nm_006425] Divided High confidence 223.463 212.875 1.04974
753 dna polymerase delta p38 subunit. [refseq;acc:nm_015584] Low confidence 202.039 196.717 1.02705
eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] Subtracted High confidence 210.946 221.225 10.279
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Divided 224.434 235.583 1.04968
rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Subtracted Low confidence 202.639 197.261 5.378
754 microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] Divided High confidence 224.434 235.583 1.04968
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Low confidence 203.246 197.894 1.02704
suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] Subtracted High confidence 210.946 221.225 10.279
tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063] Low confidence 203.545 198.176 5.369
755 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] High confidence 224.244 234.511 10.267
epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772] Divided Low confidence 206.435 201.001 1.02703
uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] High confidence 224.434 235.583 1.04968
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 4, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 4). [swissprot;acc:q16654] Subtracted Low confidence 203.545 198.176 5.369
756 40s ribosomal protein s21. [swissprot;acc:p35265] High confidence 224.244 234.511 10.267
cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] Divided 224.434 235.583 1.04968
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Low confidence 201.703 196.395 1.02703
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 3, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 3). [swissprot;acc:q15120] Subtracted 203.543 198.176 5.367
757 bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] Divided High confidence 224.434 235.583 1.04968
cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] Subtracted 224.244 234.511 10.267
epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] Divided Low confidence 211.344 205.788 1.027
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Subtracted 203.233 197.87 5.363
758 imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 198.97 193.609 5.361
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] High confidence 224.244 234.511 10.267
phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] Divided 224.434 235.583 1.04968
receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626] Low confidence 211.342 205.787 1.02699
759 bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] Subtracted High confidence 224.244 234.511 10.267
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Divided Low confidence 200.18 194.922 1.02697
osteoclast stimulating factor 1. [swissprot;acc:q92882] High confidence 231.809 243.289 1.04952
ubiquitin associated protein 2 isoform 1; ad-012 protein. [refseq;acc:nm_018449] Subtracted Low confidence 205.905 200.545 5.36
760 mitochondrial import inner membrane translocase subunit tim13 b. [swissprot;acc:q9y5l4] 203.24 197.883 5.357
plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] High confidence 224.244 234.511 10.267
transportin-sr; importin 12. [refseq;acc:nm_012470] Divided Low confidence 191.294 186.27 1.02697
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] High confidence 246.055 234.458 1.04946
761 homeobox protein nkx-2.3 (homeobox protein nkx-2.3) (homeobox protein nk-2 homolog c). [swissprot;acc:q8tau0] Low confidence 206.052 200.644 1.02695
serpin b11. [swissprot;acc:q96p15] Subtracted High confidence 224.244 234.511 10.267
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Divided 213.325 203.303 1.0493
transcription factor iib. [refseq;acc:nm_013242] Subtracted Low confidence 205.668 200.313 5.355
762 cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Divided High confidence 213.256 203.237 1.0493
chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Low confidence 213.926 208.315 1.02694
placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] Subtracted High confidence 224.244 234.511 10.267
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Low confidence 203.246 197.894 5.352
763 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Divided 213.929 208.318 1.02693
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Subtracted High confidence 224.244 234.511 10.267
heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Low confidence 208.623 213.975 5.352
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Divided High confidence 228.78 218.091 1.04901
764 homeobox protein nkx-2.5 (homeobox protein nk-2 homolog e) (cardiac- specific homeobox) (homeobox protein csx). [swissprot;acc:p52952] Low confidence 206.038 200.638 1.02691
leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] Subtracted High confidence 224.244 234.511 10.267
protein disulfide isomerase a3 precursor (ec 5.3.4.1) (disulfide isomerase er-60) (erp60) (58 kda microsomal protein) (p58) (erp57) (58 kda glucose regulated protein). [swissprot;acc:p30101] Low confidence 204.144 198.795 5.349
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Divided High confidence 222.082 211.707 1.04901
765 eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] Subtracted 243.067 232.805 10.262

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
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/