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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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