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 363 to 412 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
46 deltex 2. [refseq;acc:nm_020892] Rooted 1 27.634 43.9629 1.5909
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked 204.642 161.068 1.27053
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Rooted 0 12.53 7.48331 1.67439
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Measured 1 779.167 1390.33 1.78438
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] Squared 0 14.8562 83.274 5.60534
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] Measured 202.163 438.035 2.16674
47 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] Ranked 12941.7 18499.2 1.42943
adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Rooted 21.3967 34.6716 1.62042
chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Measured 1 779.167 1390.33 1.78438
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Rooted 27.7078 44.017 1.58861
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Squared 0 975.125 178.265 5.47009
gbp protein isoform a. [refseq;acc:nm_017870] Ranked 1 325.586 256.492 1.26938
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] Measured 0 202.156 438.016 2.16672
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Squared 1 98517.9 56927.2 1.73059
48 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Measured 0 870.482 403.196 2.15895
doc-1 related protein (doc-1r). [swissprot;acc:o75956] 1 779.167 1390.33 1.78438
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Ranked 65.4586 83.0461 1.26868
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Squared 0 960.518 176.164 5.45241
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 1 6300.2 10703.5 1.69891
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] Ranked 0 9830 6909 1.42278
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Rooted 1 27.7254 44.0299 1.58807
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] 0 15.0533 9.31487 1.61605
49 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Squared 1 28994.2 17134.8 1.69212
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Ranked 133 105 1.26667
brain protein 16. [refseq;acc:nm_016458] 0 6890.54 4854.99 1.41927
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Squared 8.10857 43.7473 5.39519
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Rooted 1 27.7254 44.0299 1.58807
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Measured 779.167 1390.33 1.78438
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] Rooted 0 14.1508 8.89106 1.59158
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Measured 72 151 2.09722
50 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Ranked 1 133 105 1.26667
cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 0 9249.73 13091.4 1.41533
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] Rooted 11.0328 6.96286 1.58452
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1 27.7254 44.0299 1.58807
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Measured 779.167 1390.33 1.78438
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] Squared 0 10.974 2.38124 4.60852
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 1 28994.2 17134.8 1.69212
transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] Measured 0 44 21 2.09524
51 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] Squared 0.872309 3.99932 4.58475
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 1 28994.2 17134.8 1.69212
importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] Ranked 0 7168 5102 1.40494
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Rooted 1 27.7254 44.0299 1.58807
nanos (fragment). [sptrembl;acc:q8wy41] 0 19.4165 12.2882 1.58009
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured 1 779.167 1390.33 1.78438
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] 0 184.422 88.5622 2.0824
spermatogenesis associated 6. [refseq;acc:nm_019073] Ranked 1 133 105 1.26667
52 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] 0 3284 4554.5 1.38688
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Measured 1 779.167 1390.33 1.78438
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 0 999.28 481.725 2.07438

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/