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