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 Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 401 to 450 of 9634 in total
Network Comparison Type  : Divided
Value Type  : Measured
Rank
description
Interaction Map
Filtered
red
network_comparison
green
101 60s ribosomal protein l37a. [swissprot;acc:p12751] Low confidence 0 535.61 1.47569 362.955
cullin homolog 2 (cul-2). [swissprot;acc:q13617] High confidence 1 2353.63 1.3705 3225.65
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] 0 1442 1.47595 977
set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Low confidence 1 5752.65 1.10037 6330.03
102 mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932] 0 248.513 1.4723 168.792
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] High confidence 1442 1.47595 977
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 1 2353.63 1.3705 3225.65
testis-specific protein tex28. [swissprot;acc:o15482] Low confidence 5060.92 1.10006 5567.34
103 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
cullin homolog 1 (cul-1). [swissprot;acc:q13616] High confidence 2353.63 1.3705 3225.65
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Low confidence 0 5106.93 1.46874 7500.75
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] High confidence 197.333 1.47298 290.667
104 musashi 2 isoform a. [refseq;acc:nm_138962] 1 4241.57 1.36996 5810.79
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 0 5106.93 1.46874 7500.75
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Low confidence 1 10618.8 1.10006 11681.3
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 0 94.9795 1.46638 139.276
105 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 461.554 1.45105 669.737
fos-related antigen 2. [swissprot;acc:p15408] High confidence 3233.86 1.46454 2208.1
musashi 1. [refseq;acc:nm_002442] 1 4241.57 1.36996 5810.79
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Low confidence 10585.5 1.09949 11638.6
106 lats homolog 1. [refseq;acc:nm_004690] 0 160 1.42539 112.25
nuclear protein ukp68. [refseq;acc:nm_024824] High confidence 1 4241.57 1.36996 5810.79
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 0 1251.66 1.45792 858.525
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Low confidence 1 7337.57 1.09789 8055.84
107 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] High confidence 4266.04 1.36977 5843.51
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 0 326.677 1.4467 472.605
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Low confidence 160 1.42539 112.25
tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881] 1 11371 1.09746 12479.2
108 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] High confidence 0 292 1.44178 421
filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] 1 4366.44 1.35116 5899.76
nanos (fragment). [sptrembl;acc:q8wy41] Low confidence 0 338.761 1.41306 478.69
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 1 10499 1.09685 11515.8
109 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] High confidence 0 100 1.44 144
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 1 4366.44 1.35116 5899.76
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Low confidence 7354.65 1.0966 8065.08
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] 0 385 1.41039 543
110 enigma protein; lim domain protein. [refseq;acc:nm_005451] 967.877 1.38222 1337.82
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] 1 7206.99 1.09572 7896.81
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] High confidence 4366.44 1.35116 5899.76
spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] 0 1833 1.43863 2637
111 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Low confidence 1 11285.3 1.0937 10318.5
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] High confidence 4366.44 1.35116 5899.76
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 0 2965.5 1.43747 2063
Low confidence 1763.83 1.37838 1279.64
112 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 1 11285.3 1.0937 10318.5
lats homolog 1. [refseq;acc:nm_004690] High confidence 0 160 1.42539 112.25
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Low confidence 1392.08 1.37602 1011.67
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] High confidence 1 4366.44 1.35116 5899.76
113 filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Low confidence 11285.3 1.0937 10318.5

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/