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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 351 to 400 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
44 KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Ranked Subtracted 332.874 267.246 65.628
MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Squared 110342 184298 73956
45 no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Divided 129597 73157.5 1.77148
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Subtracted 110342 184298 73956
FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Ranked Divided 204.641 161.051 1.27066
FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Rooted Subtracted 60.875 77.7152 16.8402
GNB3 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Divided 40.081 25.1546 1.59339
GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Measured 1926.69 1056.02 1.82448
KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Ranked Subtracted 332.874 267.246 65.628
PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Measured 27642.5 22440.4 5202.1
46 ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Squared Divided 129597 73157.5 1.77148
CPSF4 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Measured Subtracted 24896.4 20431.7 4464.7
DTX2 deltex 2. [refseq;acc:nm_020892] Rooted Divided 27.634 43.9629 1.5909
FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked 204.642 161.068 1.27053
MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Rooted Subtracted 137.446 120.823 16.623
NEURL neuralized-like. [refseq;acc:nm_004210] Ranked 332.326 266.948 65.378
NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Measured Divided 779.167 1390.33 1.78438
PAPOLA poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Squared Subtracted 210445 136779 73666
47 no value ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Divided 98517.9 56927.2 1.73059
CHD3 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Measured 779.167 1390.33 1.78438
DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Rooted 27.7078 44.017 1.58861
EXOC2 exocyst complex component sec5. [swissprot;acc:q96kp1] Squared Subtracted 210335 136716 73619
KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Measured 24896.4 20431.7 4464.7
MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Rooted 137.446 120.823 16.623
TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Ranked Divided 325.586 256.492 1.26938
TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Subtracted 350 290 60
48 no value melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Rooted 137.446 120.823 16.623
CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Measured Divided 779.167 1390.33 1.78438
GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Ranked 65.4586 83.0461 1.26868
LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Squared 6300.2 10703.5 1.69891
PAPOLG poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Subtracted 210199 136638 73561
PBK 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 Divided 27.7254 44.0299 1.58807
TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Ranked Subtracted 350 290 60
WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Measured 24806.9 20369.9 4437
49 ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Ranked Divided 133 105 1.26667
CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Measured Subtracted 24806.9 20369.9 4437
CSTF3 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Squared 201896 131906 69990
DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Ranked 350 290 60
KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Rooted Divided 27.7254 44.0299 1.58807
MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Subtracted 137.446 120.823 16.623
NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Measured Divided 779.167 1390.33 1.78438
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Squared 28994.2 17134.8 1.69212
50 no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted 173408 242989 69581
ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Ranked Divided 133 105 1.26667
CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Squared 28994.2 17134.8 1.69212
CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Ranked Subtracted 350 290 60
CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Measured 24473.9 20127.8 4346.1
KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Rooted Divided 27.7254 44.0299 1.58807
MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Subtracted 137.446 120.823 16.623
NEUROD1 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Measured Divided 779.167 1390.33 1.78438

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
- Hugo is the HGNC identifier if it exists
- 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/