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 Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1800 to 1849 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
113 glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Squared Divided 0 387.336 770.962 1.99042
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Ranked 1 332.874 267.246 1.24557
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Subtracted 0 8335.82 10228.3 1892.48
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Squared Divided 1 19321 12542.6 1.54043
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Rooted 0 72.1137 56.7758 1.27015
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Ranked 5673.33 6797.56 1.19816
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Subtracted 1 194.372 234.204 39.832
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Measured Divided 0 160 112.25 1.42539
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Subtracted 3117.17 2833.94 283.23
114 60s ribosomal protein l37a. [swissprot;acc:p12751] 305.45 26.1599 279.29
autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Squared 1 67438.6 40697 26741.6
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Ranked 229.818 267.265 37.447
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Rooted Divided 80.4705 101.526 1.26165
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] Ranked 0 8871.11 10603.2 1.19525
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Squared Subtracted 5868.74 4797.35 1071.39
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Measured 1 13768.2 11466 2302.2
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Divided 0 671.769 472.945 1.4204
guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Rooted Subtracted 1 40.225 24.7051 15.5199
huntingtin interacting protein c. [refseq;acc:nm_012272] Measured Divided 4300.47 5807.72 1.35048
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Rooted Subtracted 0 11.0051 15.3166 4.3115
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Ranked Divided 1 332.874 267.246 1.24557
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Subtracted 0 19355 17469.2 1885.8
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Squared Divided 1 19321 12542.6 1.54043
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Rooted 0 14.7363 18.7165 1.27009
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] Squared 35.0828 69.7867 1.9892
115 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] Measured Subtracted 305.45 26.1599 279.29
28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Divided 1 21185 28492 1.34491
40s ribosomal protein s26. [swissprot;acc:p02383] Rooted Subtracted 0 9.92134 5.66499 4.25635
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] Squared Divided 105.615 53.4024 1.97772
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Rooted Subtracted 1 21.4476 36.9459 15.4983
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Squared Divided 19321 12542.6 1.54043
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Ranked Subtracted 0 11124.8 13005.3 1880.5
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Rooted Divided 18.4959 14.5738 1.26912
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Ranked Subtracted 1 277.546 240.461 37.085
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Divided 332.874 267.246 1.24557
pnas-18. [sptrembl;acc:q9bzu3] Measured Subtracted 13680.5 11409.6 2270.9
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Squared 0 6027.87 7086.08 1058.21
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 1 72886.3 98544.5 25658.2
spermatogenesis associated 6. [refseq;acc:nm_019073] Rooted Divided 80.4705 101.526 1.26165
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] Ranked 0 18662.8 15627 1.19427
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] Measured 385 543 1.41039
116 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 668 475 1.40632
amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Rooted 1 80.4705 101.526 1.26165
cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Measured Subtracted 0 1382.5 1107 275.5
dead-box protein. [refseq;acc:nm_018665] Squared Divided 37.7545 19.3759 1.94853
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Ranked Subtracted 11123.4 13000.1 1876.7
elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] Rooted Divided 9.7842 7.75282 1.26202
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Subtracted 1 40.6302 25.4452 15.185
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Ranked Divided 268.565 334.483 1.24545
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Subtracted 208.52 171.595 36.925

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/