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 green Gene Network Comparison Type Value Type Filtered Interaction Map red network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 77072 in total
Rank
description
green
Network Comparison Type
Value Type
Filtered
Interaction Map
red
network_comparison
16 protein kinase, lysine deficient 3. [refseq;acc:nm_020922] 221.042 Divided Squared 0 Low confidence 4.89136 45.1903
704.5 Measured 125 5.636
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] 15 High confidence 1 15
protein x 0004. [refseq;acc:nm_016301] 179.56 Squared 1 1688.58 9.40399
871 Measured 2671 3.06659
ptd016 protein. [refseq;acc:nm_016125] 11234 Subtracted Ranked 0 18050 6816
serpin b12. [swissprot;acc:q96p63] 1.18697 Divided Rooted 10.2928 8.67149
sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796] 12191.6 Subtracted Ranked Low confidence 7435.56 4756.04
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 247.246 Divided 1 305.472 1.2355
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 49.1529 Rooted 38.4152 1.27952
vps10 domain-containing receptor sorcs1 precursor (hsorcs). [swissprot;acc:q8wy21] 9808 Subtracted Measured 0 8926.33 881.67
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 29.5127 Divided Rooted 1 High confidence 51.6817 1.75117
17 ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] 12473 Subtracted Measured 0 11223 1250
bcl2-related ovarian killer. [refseq;acc:nm_032515] 223.235 Ranked 1 Low confidence 265.638 42.403
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 42114.6 Squared 0 High confidence 25050 17064.6
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 75.447 Divided Ranked 1 56.7841 1.32866
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 182.638 Subtracted Rooted 203.673 21.035
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 441 Divided Squared 50.0828 8.80542
1365 Measured 460 2.96739
ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08] 5837.83 Subtracted 0 Low confidence 4959.42 878.41
ero1-like. [refseq;acc:nm_014584] 20536 Ranked High confidence 13853 6683
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 Divided 11543 1.69451
Subtracted Low confidence 4731
gbp protein isoform a. [refseq;acc:nm_017870] 247.213 Divided 1 305.399 1.23537
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 336.182 Subtracted High confidence 266.864 69.318
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 17572.7 Measured Low confidence 15464.1 2108.6
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 9.43398 Rooted 0 0 9.43398
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 159767 Squared 1 122475 37292
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 1.2188 Divided Rooted 0 High confidence 10.3085 8.45791
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] 47.7352 Subtracted 1 Low confidence 31.9296 15.8056
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] 5266.67 Divided Ranked 0 8082.33 1.53462
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 18168.9 Subtracted Measured 1 High confidence 24255.7 6086.8
mitochondrial solute carrier protein. [refseq;acc:nm_145305] 28492 Divided Low confidence 21185 1.34491
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 58 0 High confidence 859 14.8103
necdin. [swissprot;acc:q99608] 129762 Subtracted Squared 1 219048 89286
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 0 Rooted 0 12.4097 12.4097
protein x 0004. [refseq;acc:nm_016301] 29.5127 Divided 1 51.6817 1.75117
ptd016 protein. [refseq;acc:nm_016125] 5.90864 Squared 0 Low confidence 0.213018 27.7377
12.5698 Rooted 5.47723 2.29492
158 Measured 30 5.26667
putative dynein light chain protein dj8b22.1. [swissprot;acc:q9y3p0] 46849.7 Subtracted Squared 56144.4 9294.7
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 0.00001 Divided High confidence 0.0766864 7668.64
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 49.2633 Rooted 1 Low confidence 38.5678 1.27732
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] 475045 Squared 333506 1.4244
18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 245.247 Ranked High confidence 185.678 1.32082
60s ribosomal protein l37a. [swissprot;acc:p12751] 26.1599 Measured 0 305.45 11.6763
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 0.52284 Squared 439.709 841.001
anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] 14167 Subtracted Measured 15411.3 1244.3
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 60.0707 Divided Rooted 9.20014 6.52932
camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] 0.0854438 Squared Low confidence 2.31976 27.1495

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/