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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Filtered Gene Rank Value Type description Network Comparison Type green Interaction Map red network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 29840 in total
Filtered  : 0
Interaction Map  : High confidence
Rank
Value Type
description
Network Comparison Type
green
red
network_comparison
63 Squared protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Divided 0.365145 1.24091 3.3984
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Subtracted 96418.4 99229.9 2811.5
Rooted dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Divided 12.6095 18.1049 1.43581
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Subtracted 31.257 37.9737 6.7167
64 Measured importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] 1068 607 461
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] Divided 18 0.00001 1800000
Ranked hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] Subtracted 11134.8 8152.55 2982.25
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] Divided 20387 15264 1.33563
Squared cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Subtracted 11676.7 14470.6 2793.9
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Divided 15.2519 50.8715 3.33542
Rooted muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 22.5496 15.7225 1.43422
phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Subtracted 31.257 37.9737 6.7167
65 Measured muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 861.814 420.365 441.449
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Divided 0.00001 18 1800000
Ranked e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 10406.3 7853.67 1.32502
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Subtracted 11453 8519.83 2933.17
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] Divided 15.1833 50.642 3.33538
metaxin 1. [swissprot;acc:q13505] Subtracted 3429.64 6149.89 2720.25
Rooted 60s ribosomal protein l21. [swissprot;acc:p46778] Divided 29.2291 20.5734 1.42072
sedlin. [swissprot;acc:o14582] Subtracted 6.55744 0 6.55744
66 Measured fibrillin 3. [refseq;acc:nm_032447] 13809 14246 437
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Divided 385.626 688.436 1.78524
Ranked heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 15180 11461 1.32449
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] Subtracted 6909 9830 2921
Squared dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Divided 558.241 1797.76 3.2204
tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] Subtracted 5963.73 8660.1 2696.37
Rooted oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided 21.9983 30.9855 1.40854
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Subtracted 6.55744 0 6.55744
67 Measured filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Divided 898 1603 1.78508
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Subtracted 4320.09 4755.32 435.23
Ranked presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] Divided 14291.5 10793.5 1.32408
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Subtracted 11823.3 8932.56 2890.74
Squared filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Divided 190.865 608.191 3.1865
udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] Subtracted 3763.18 6123.28 2360.1
Rooted isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Divided 15.3166 11.0051 1.39177
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Subtracted 14.4058 7.90063 6.50517
68 Measured folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 6019.79 6452.66 432.87
protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] Divided 351.772 198.964 1.76802
Ranked 40s ribosomal protein s26. [swissprot;acc:p02383] Subtracted 17098 14269.7 2828.3
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Divided 11823.3 8932.56 1.32362
Squared mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0.00001 31.36 3136000
udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310] Subtracted 3763.18 6123.28 2360.1
Rooted alpha crystallin a chain. [swissprot;acc:p02489] Divided 8.63381 6.22183 1.38766
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Subtracted 87.2238 93.6109 6.3871
69 Measured dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Divided 2804 1593 1.7602
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Subtracted 139 570 431
Ranked collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Divided 10174.1 7704.7 1.32051
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Subtracted 13464.8 16290.7 2825.9
Squared protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] Divided 50.7408 16.2406 3.12432
udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133] Subtracted 3763.18 6123.28 2360.1

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/