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