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

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/