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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Gene Filtered Rank green network_comparison Interaction Map Value Type description red Network Comparison Type
Results: HTML CSV LaTeX Showing element 501 to 550 of 38536 in total
Filtered  : 0
Network Comparison Type  : Divided
Rank
green
network_comparison
Interaction Map
Value Type
description
red
63 75.6508 2.03842 Low confidence Measured laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942] 154.208
173.307 3.92038 Squared synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 44.2067
11453 1.34428 High confidence Ranked oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 8519.83
15783.5 1.27551 Low confidence 60s ribosomal protein l37a. [swissprot;acc:p12751] 12374.3
64 15.2519 3.33542 High confidence Squared tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 50.8715
18 1800000 Measured phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] 0.00001
22.5496 1.43422 Rooted muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 15.7225
23.6984 2.03615 Low confidence Measured dna helicase homolog (fragment). [sptrembl;acc:q9y645] 48.2534
66 1.44645 Rooted anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] 45.6289
173.244 3.88974 Squared sedlin. [swissprot;acc:o14582] 44.5387
11356 1.2736 Ranked selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 14463
20387 1.33563 High confidence similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 15264
65 0.00001 1800000 Measured rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 18
10.4958 1.43105 Low confidence Rooted transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] 7.33436
15.1833 3.33538 High confidence Squared 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 50.642
29.2291 1.42072 Rooted 60s ribosomal protein l21. [swissprot;acc:p46778] 20.5734
47.3595 3.55848 Low confidence Squared l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [swissprot;acc:p00338] 13.3089
923.065 1.98228 Measured bet5 homolog (multiple myeloma protein 2) (mum-2). [swissprot;acc:q9y5r8] 465.658
10406.3 1.32502 High confidence Ranked e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 7853.67
12943.5 1.27245 Low confidence alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 10172.1
66 21.9983 1.40854 High confidence Rooted oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 30.9855
26.828 1.4185 Low confidence elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9] 18.9129
127.516 3.47056 Squared nadh-ubiquinone oxidoreductase mlrq subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-mlrq) (ci-mlrq). [swissprot;acc:o00483] 36.7422
142.981 1.89874 Measured tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 271.484
385.626 1.78524 High confidence soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] 688.436
558.241 3.2204 Squared dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 1797.76
10030.4 1.26584 Low confidence Ranked kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] 7923.89
15180 1.32449 High confidence heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 11461
67 12.9538 1.41698 Low confidence Rooted alpha 2 globin. [refseq;acc:nm_000517] 18.3553
15.2519 3.33542 Squared tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 50.8715
15.3166 1.39177 High confidence Rooted isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 11.0051
142.417 1.89769 Low confidence Measured 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 270.264
190.865 3.1865 High confidence Squared filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 608.191
898 1.78508 Measured 1603
14291.5 1.32408 Ranked presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 10793.5
14697.6 1.26309 Low confidence dynamin-like 120 kda protein, mitochondrial precursor (optic atrophy 1 gene protein). [swissprot;acc:o60313] 11636.2
68 0.00001 3136000 High confidence Squared mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 31.36
8.63381 1.38766 Rooted alpha crystallin a chain. [swissprot;acc:p02489] 6.22183
12.9627 1.41651 Low confidence hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096] 18.3618
15.1833 3.33538 Squared 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 50.642
351.772 1.76802 High confidence Measured protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] 198.964
734 1.86294 Low confidence nadh-ubiquinone oxidoreductase mlrq subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-mlrq) (ci-mlrq). [swissprot;acc:o00483] 394
9824.6 1.25899 Ranked repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 7803.58
11823.3 1.32362 High confidence purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 8932.56
69 12.9659 1.41635 Low confidence Rooted myoglobin. [swissprot;acc:p02144] 18.3642
13.5207 1.38596 High confidence cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 18.7392
50.7408 3.12432 Squared protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] 16.2406
70.5 1.82979 Low confidence Measured tubulointerstitial nephritis antigen. [refseq;acc:nm_014464] 129
253.857 3.26573 Squared tolloid-like 1. [refseq;acc:nm_012464] 77.7335
2804 1.7602 High confidence Measured dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 1593

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/