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 Value Type Rank Interaction Map Filtered description red Network Comparison Type green network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 29840 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
Filtered
description
red
Network Comparison Type
green
network_comparison
13 1 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 398.5 Divided 1281.5 3.21581
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] 21591.5 Subtracted 27904.5 6313
14 0 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 10817.1 12125.1 1308
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 130.512 Divided 6.50325 20.0687
1 myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 21591.5 Subtracted 27904.5 6313
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 398.5 Divided 1281.5 3.21581
15 0 succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] 10 156 15.6
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 7981.68 Subtracted 6685.11 1296.57
1 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 21591.5 27904.5 6313
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 2671 Divided 871 3.06659
16 0 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 8852.4 Subtracted 7572.88 1279.52
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] 1 Divided 15 15
1 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 24260.3 Subtracted 18172.1 6088.2
protein x 0004. [refseq;acc:nm_016301] 2671 Divided 871 3.06659
17 0 ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] 11223 Subtracted 12473 1250
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 859 Divided 58 14.8103
1 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 460 1365 2.96739
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 24255.7 Subtracted 18168.9 6086.8
18 0 60s ribosomal protein l37a. [swissprot;acc:p12751] 305.45 Divided 26.1599 11.6763
anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] 15411.3 Subtracted 14167 1244.3
1 microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 24255.7 18168.9 6086.8
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 677.5 Divided 1865.5 2.75351
19 0 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] 305.45 26.1599 11.6763
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 1593 Subtracted 2804 1211
1 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 24250 18164.9 6085.1
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 677.5 Divided 1865.5 2.75351
20 0 ero1-like. [refseq;acc:nm_014584] 82 0.00001 8200000
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] 8763 Subtracted 7608 1155
1 gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 23421.5 17580.4 5841.1
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 677.5 Divided 1865.5 2.75351
21 0 swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] 6804.88 Subtracted 5690.63 1114.25
syntaxin 10 (syn10). [swissprot;acc:o60499] 118.878 Divided 17.6611 6.73106
1 ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 677.5 1865.5 2.75351
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 23693.7 Subtracted 18263 5430.7
22 0 similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 60 Divided 0.00001 6000000
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] 31122 Subtracted 30022.4 1099.6
1 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 23693.7 18263 5430.7
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 677.5 Divided 1865.5 2.75351
23 0 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 6596.23 Subtracted 5540.2 1056.03
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] 0.00001 Divided 59 5900000
1 gbp protein isoform a. [refseq;acc:nm_017870] 699.76 1894.39 2.7072
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 23693.7 Subtracted 18263 5430.7
24 0 fos-related antigen 2. [swissprot;acc:p15408] 3233.86 2208.1 1025.76
ptd016 protein. [refseq;acc:nm_016125] 30 Divided 158 5.26667
1 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 23693.7 Subtracted 18263 5430.7
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 950.561 Divided 2108.52 2.21818
25 0 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] 459.5 Subtracted 1377 917.5
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 148 Divided 773 5.22297
1 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 1833.01 892.67 2.0534
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 23693.7 Subtracted 18263 5430.7

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/