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 Rank Value Type Network Comparison Type description Filtered green network_comparison red Interaction Map
Results: HTML CSV LaTeX Showing element 101 to 150 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
Value Type
description
green
network_comparison
red
Interaction Map
13 Squared carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 242799 1.63062 395912 Low confidence
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 388.696 10.3414 37.5863 High confidence
Rooted 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] 52.5277 1.33896 39.2301 Low confidence
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 35.798 1.79326 19.9625 High confidence
14 Measured ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 1281.5 3.21581 398.5
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] 2998.1 1.51983 1972.65 Low confidence
Ranked cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 75.3531 1.32952 56.6768 High confidence
vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] 29.1831 1.30207 37.9984 Low confidence
Squared atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 4959.41 1.56161 7744.68
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 388.696 10.3414 37.5863 High confidence
Rooted 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] 52.5401 1.33864 39.2489 Low confidence
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 35.798 1.79326 19.9625 High confidence
15 Measured trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] 3007.85 1.51612 1983.91 Low confidence
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 871 3.06659 2671 High confidence
Ranked microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 75.3948 1.32914 56.7244
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 202.362 1.26035 255.046 Low confidence
Squared sperm associated antigen 7. [refseq;acc:nm_004890] 136572 1.53438 209554
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 179.56 9.40399 1688.58 High confidence
Rooted 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] 52.9343 1.32836 39.8493 Low confidence
gbp protein isoform a. [refseq;acc:nm_017870] 42.4773 1.77158 23.9771 High confidence
16 Measured 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 28492 1.34491 21185 Low confidence
protein x 0004. [refseq;acc:nm_016301] 871 3.06659 2671 High confidence
Ranked microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 75.3954 1.32913 56.7252
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 247.246 1.2355 305.472 Low confidence
Squared bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 475119 1.42441 333556
protein x 0004. [refseq;acc:nm_016301] 179.56 9.40399 1688.58 High confidence
Rooted tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 49.1529 1.27952 38.4152 Low confidence
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 29.5127 1.75117 51.6817 High confidence
17 Measured dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 1365 2.96739 460
mitochondrial solute carrier protein. [refseq;acc:nm_145305] 28492 1.34491 21185 Low confidence
Ranked cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 75.447 1.32866 56.7841 High confidence
gbp protein isoform a. [refseq;acc:nm_017870] 247.213 1.23537 305.399 Low confidence
Squared dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 441 8.80542 50.0828 High confidence
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] 475045 1.4244 333506 Low confidence
Rooted protein x 0004. [refseq;acc:nm_016301] 29.5127 1.75117 51.6817 High confidence
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 49.2633 1.27732 38.5678 Low confidence
18 Measured cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 7251 1.32027 5492.04
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 1865.5 2.75351 677.5 High confidence
Ranked 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 245.247 1.32082 185.678
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] 247.169 1.2352 305.303 Low confidence
Squared nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 473408 1.42416 332411
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 823.69 7.58176 108.641 High confidence
Rooted dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 36.9459 1.72261 21.4476
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 55.937 1.25937 44.4168 Low confidence
19 Measured 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] 3915.4 1.29112 3032.56
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 1865.5 2.75351 677.5 High confidence
Ranked glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 245.247 1.32082 185.678
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] 246.824 1.23387 304.548 Low confidence
Squared microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 823.69 7.58176 108.641 High confidence
vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] 473408 1.42416 332411 Low confidence

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/