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 green red network_comparison
Results: HTML CSV LaTeX Showing element 101 to 150 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Value Type
Interaction Map
green
red
network_comparison
13 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Rooted High confidence 35.798 19.9625 1.79326
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Measured Low confidence 2959.19 1927.68 1.5351
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Ranked 29.1831 37.9984 1.30207
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] High confidence 212.554 288.754 1.3585
14 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Squared Low confidence 4959.41 7744.68 1.56161
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Ranked High confidence 75.3531 56.6768 1.32952
cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] Rooted Low confidence 52.5401 39.2489 1.33864
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Measured High confidence 1281.5 398.5 3.21581
Squared 388.696 37.5863 10.3414
Rooted 35.798 19.9625 1.79326
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Measured Low confidence 2998.1 1972.65 1.51983
vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Ranked 29.1831 37.9984 1.30207
15 cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] Rooted 52.9343 39.8493 1.32836
gbp protein isoform a. [refseq;acc:nm_017870] High confidence 42.4773 23.9771 1.77158
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Ranked 75.3948 56.7244 1.32914
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Low confidence 202.362 255.046 1.26035
sperm associated antigen 7. [refseq;acc:nm_004890] Squared 136572 209554 1.53438
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Measured 3007.85 1983.91 1.51612
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] High confidence 871 2671 3.06659
Squared 179.56 1688.58 9.40399
16 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Measured Low confidence 28492 21185 1.34491
bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Squared 475119 333556 1.42441
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Ranked High confidence 75.3954 56.7252 1.32913
protein x 0004. [refseq;acc:nm_016301] Measured 871 2671 3.06659
Squared 179.56 1688.58 9.40399
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Ranked Low confidence 247.246 305.472 1.2355
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Rooted 49.1529 38.4152 1.27952
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] High confidence 29.5127 51.6817 1.75117
17 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Ranked 75.447 56.7841 1.32866
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Measured 1365 460 2.96739
Squared 441 50.0828 8.80542
gbp protein isoform a. [refseq;acc:nm_017870] Ranked Low confidence 247.213 305.399 1.23537
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Measured 28492 21185 1.34491
protein x 0004. [refseq;acc:nm_016301] Rooted High confidence 29.5127 51.6817 1.75117
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Low confidence 49.2633 38.5678 1.27732
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Squared 475045 333506 1.4244
18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Ranked High confidence 245.247 185.678 1.32082
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Measured Low confidence 7251 5492.04 1.32027
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Rooted High confidence 36.9459 21.4476 1.72261
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Ranked Low confidence 247.169 305.303 1.2352
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Squared 473408 332411 1.42416
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Rooted 55.937 44.4168 1.25937
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Measured High confidence 1865.5 677.5 2.75351
Squared 823.69 108.641 7.58176
19 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] Measured Low confidence 3915.4 3032.56 1.29112
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Ranked High confidence 245.247 185.678 1.32082
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Measured 1865.5 677.5 2.75351
Squared 823.69 108.641 7.58176
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Rooted Low confidence 66.8994 53.5555 1.24916
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] High confidence 43.561 25.6987 1.69507

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/