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 description Network Comparison Type Interaction Map Filtered Value Type red network_comparison green
Results: HTML CSV LaTeX Showing element 501 to 550 of 77072 in total
Rank
description
Network Comparison Type
Interaction Map
Filtered
Value Type
red
network_comparison
green
16 protein kinase, lysine deficient 3. [refseq;acc:nm_020922] Divided Low confidence 0 Measured 125 5.636 704.5
Squared 4.89136 45.1903 221.042
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] High confidence Measured 1 15 15
protein x 0004. [refseq;acc:nm_016301] 1 2671 3.06659 871
Squared 1688.58 9.40399 179.56
ptd016 protein. [refseq;acc:nm_016125] Subtracted 0 Ranked 18050 6816 11234
serpin b12. [swissprot;acc:q96p63] Divided Rooted 10.2928 8.67149 1.18697
sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796] Subtracted Low confidence Ranked 7435.56 4756.04 12191.6
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Divided 1 305.472 1.2355 247.246
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Rooted 38.4152 1.27952 49.1529
vps10 domain-containing receptor sorcs1 precursor (hsorcs). [swissprot;acc:q8wy21] Subtracted 0 Measured 8926.33 881.67 9808
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Divided High confidence 1 Rooted 51.6817 1.75117 29.5127
17 ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] Subtracted 0 Measured 11223 1250 12473
bcl2-related ovarian killer. [refseq;acc:nm_032515] Low confidence 1 Ranked 265.638 42.403 223.235
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] High confidence 0 Squared 25050 17064.6 42114.6
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Divided 1 Ranked 56.7841 1.32866 75.447
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Subtracted Rooted 203.673 21.035 182.638
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Divided Measured 460 2.96739 1365
Squared 50.0828 8.80542 441
ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08] Subtracted Low confidence 0 Measured 4959.42 878.41 5837.83
ero1-like. [refseq;acc:nm_014584] High confidence Ranked 13853 6683 20536
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Divided 11543 1.69451 6812
Subtracted Low confidence 4731
gbp protein isoform a. [refseq;acc:nm_017870] Divided 1 305.399 1.23537 247.213
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Subtracted High confidence 266.864 69.318 336.182
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Low confidence Measured 15464.1 2108.6 17572.7
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 Rooted 0 9.43398 9.43398
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 1 Squared 122475 37292 159767
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Divided High confidence 0 Rooted 10.3085 8.45791 1.2188
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Subtracted Low confidence 1 31.9296 15.8056 47.7352
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Divided 0 Ranked 8082.33 1.53462 5266.67
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Subtracted High confidence 1 Measured 24255.7 6086.8 18168.9
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Divided Low confidence 21185 1.34491 28492
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] High confidence 0 859 14.8103 58
necdin. [swissprot;acc:q99608] Subtracted 1 Squared 219048 89286 129762
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 0 Rooted 12.4097 12.4097 0
protein x 0004. [refseq;acc:nm_016301] Divided 1 51.6817 1.75117 29.5127
ptd016 protein. [refseq;acc:nm_016125] Low confidence 0 Measured 30 5.26667 158
Squared 0.213018 27.7377 5.90864
Rooted 5.47723 2.29492 12.5698
putative dynein light chain protein dj8b22.1. [swissprot;acc:q9y3p0] Subtracted Squared 56144.4 9294.7 46849.7
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Divided High confidence 0.0766864 7668.64 0.00001
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Low confidence 1 Rooted 38.5678 1.27732 49.2633
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Squared 333506 1.4244 475045
18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] High confidence Ranked 185.678 1.32082 245.247
60s ribosomal protein l37a. [swissprot;acc:p12751] 0 Measured 305.45 11.6763 26.1599
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Squared 439.709 841.001 0.52284
anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] Subtracted Measured 15411.3 1244.3 14167
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Divided Rooted 9.20014 6.52932 60.0707
camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] Low confidence Measured 99 5.21053 19

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/