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 7412 to 7461 of 77072 in total
Rank
description
Value Type
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
232 presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] Rooted Divided Low confidence 0 22.7465 20.4322 1.11327
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Measured 1 9465.72 10081.6 1.06506
rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Squared High confidence 42411.6 55802.1 1.31573
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Rooted Subtracted Low confidence 0 19.6485 23.2284 3.5799
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Ranked Divided High confidence 1 239.336 267.879 1.11926
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Rooted Low confidence 65.5878 69.373 1.05771
transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] Squared 53023.6 48351.4 1.09663
tubby protein homolog. [swissprot;acc:p50607] Measured Subtracted 0 2148.64 2390.13 241.49
udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] High confidence 1 9649.61 11053.5 1403.89
valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] Squared Low confidence 51669.9 47219.1 4450.8
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] Divided 0 388.064 307.101 1.26364
zinc finger protein 286. [swissprot;acc:q9hbt8] Measured 2351.96 1969.01 1.19449
zinc finger protein 33a (zinc finger protein kox31) (ha0946). [swissprot;acc:q06730] Ranked 4255.19 4852.02 1.14026
233 60s acidic ribosomal protein p1. [swissprot;acc:p05386] High confidence 9586.97 10560 1.1015
60s ribosomal protein l15. [swissprot;acc:p39030] Rooted Subtracted 19.482 17.0546 2.4274
60s ribosomal protein l7. [swissprot;acc:p18124] Ranked 1 235.727 259.984 24.257
acrc protein; putative nuclear protein. [refseq;acc:nm_052957] Low confidence 0 10129.7 11238.6 1108.9
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] Measured High confidence 6158 6303 145
bet3 homolog. [swissprot;acc:o43617] Rooted Low confidence 1 75.2506 79.2999 4.0493
brca1 associated protein. [refseq;acc:nm_006768] 0 20.1729 23.7444 3.5715
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Measured 2146.53 2387.52 240.99
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Squared Divided High confidence 5294.83 3966.41 1.33492
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Measured Low confidence 1 10519.4 9877.88 1.06495
general transcription factor iiic, polypeptide 3, 102kda; general transcription factor iiic, polypeptide 3 (102kd); transcription factor iiic, 102 kd. [refseq;acc:nm_012086] Rooted 66.7175 70.568 1.05771
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Squared Subtracted 53244.4 48813.4 4431
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] High confidence 41502.9 30836.8 10666.1
histone h2b.e (h2b/e). [swissprot;acc:q99879] 0 7090.8 7294.33 203.53
huntingtin interacting protein c. [refseq;acc:nm_012272] Rooted Divided 22.1446 19.7536 1.12104
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Ranked 1 239.32 267.842 1.11918
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Measured 0 348.823 399.534 1.14538
map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Squared 1 42411.6 55802.1 1.31573
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Rooted 137.446 120.823 1.13758
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Subtracted 95.0526 85.3206 9.732
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Measured Divided 9035 7279.6 1.24114
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Ranked Low confidence 209.649 200.129 1.04757
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Subtracted 201.41 191.974 9.436
rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Measured High confidence 9649.61 11053.5 1403.89
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Ranked 0 10367 9320.25 1046.75
sec14-like protein 2 (alpha-tocopherol associated protein) (tap) (htap) (supernatant protein factor) (spf) (squalene transfer protein). [swissprot;acc:o76054] Measured Low confidence 1 9272.87 9795.53 522.66
serine/threonine protein kinase 12 (ec 2.7.1.37) (aurora- and ipl1- like midbody-associated protein 1) (aim-1) (aurora/ipl1-related kinase 2) (aurora-related kinase 2) (stk-1) (aurora-b). [swissprot;acc:q96gd4] Squared Divided 50164 45786.3 1.09561
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Subtracted 0 1576.49 2474.6 898.11
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] Divided 388.895 308.256 1.2616
zinc finger protein 347 (zinc finger 1111). [swissprot;acc:q96se7] Ranked 4255.83 4852.69 1.14025
zinc finger protein 426; hypothetical protein mgc2663. [refseq;acc:nm_024106] Rooted 45.2561 40.6622 1.11298
zinc finger protein 7 (zinc finger protein kox4) (zinc finger protein hf.16). [swissprot;acc:p17097] Measured 2351.96 1969.01 1.19449
234 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 1 7647.22 8143.47 1.06489
40s ribosomal protein s23. [swissprot;acc:p39028] Ranked Subtracted High confidence 243.944 268.195 24.251
alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] Rooted Divided Low confidence 65.5904 69.3751 1.0577
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Ranked High confidence 287.41 256.835 1.11905
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Measured Subtracted Low confidence 0 2128.53 2368.14 239.61

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/