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 580 to 629 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
37 dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] Squared Subtracted 0 32413.7 38271.3 5857.6
dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Ranked 12128.3 7533.33 4594.97
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] 1 266.716 333.165 66.449
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Measured Divided 1836.76 907.763 2.02339
Rooted 40.2805 24.3691 1.65293
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Measured Subtracted 23693.7 18263 5430.7
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Rooted 26.0288 43.1914 17.1626
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] 0 16.3095 25.3969 9.0874
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Squared Divided 1 106226 192141 1.80879
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Ranked 322 253 1.27273
small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678] Rooted 0 4.83477 9.39626 1.94348
trs85 homolog. [swissprot;acc:q9y2l5] Squared Subtracted 1 227160 146079 81081
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Measured 0 5202.89 4550.64 652.25
38 cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] Ranked Divided 7230 10771 1.48976
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Measured Subtracted 5497.01 6127.24 630.23
ero1-like. [refseq;acc:nm_014584] Rooted 9.05539 0 9.05539
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Squared Divided 4.84 0.52284 9.25713
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Ranked Subtracted 1 266.933 333.281 66.348
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Measured Divided 1836.76 907.774 2.02337
Rooted 40.2804 24.3692 1.65292
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Measured Subtracted 23693.7 18263 5430.7
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Ranked Divided 322 253 1.27273
p28 ing5. [refseq;acc:nm_032329] Subtracted 0 12124.8 7562.05 4562.75
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Squared Divided 1 106226 192141 1.80879
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Rooted Subtracted 26.0288 43.1914 17.1626
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] Divided 0 3.62029 6.97663 1.92709
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Squared Subtracted 110701 116507 5806
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] 1 226186 145568 80618
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Measured Divided 0 320.012 120.429 2.65727
39 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] Ranked Subtracted 6313.38 10621.4 4308.02
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Squared 1 226186 145568 80618
ero1-like. [refseq;acc:nm_014584] Ranked Divided 0 13853 20536 1.48242
ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Rooted Subtracted 1 26.0288 43.1914 17.1626
guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Measured Divided 1836.8 907.903 2.02312
Rooted 40.28 24.37 1.65285
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Ranked Subtracted 268.565 334.483 65.918
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Measured 23693.7 18263 5430.7
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Divided 0 482.426 192.295 2.50878
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Squared 1 106226 192141 1.80879
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Rooted Subtracted 0 30.9855 21.9983 8.9872
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Measured 973.698 1601.52 627.822
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Rooted Divided 7.90063 14.4058 1.82337
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Ranked 1 322 253 1.27273
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Squared Subtracted 0 32743.7 27000 5743.7
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Divided 43.8625 5.33358 8.22384
40 60s ribosomal protein l21. [swissprot;acc:p46778] Rooted Subtracted 20.5734 29.2291 8.6557
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] Divided 24.454 13.5647 1.80277
cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Squared Subtracted 1 222655 143584 79071
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Divided 144940 81169.7 1.78564
deltex 2. [refseq;acc:nm_020892] Ranked Subtracted 333.144 267.393 65.751

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/