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 Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 373 to 422 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
red
network_comparison
green
47 KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Subtracted Measured 24896.4 4464.7 20431.7
MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Rooted 137.446 16.623 120.823
TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Divided Ranked 325.586 1.26938 256.492
TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Subtracted 350 60 290
48 no value melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Rooted 137.446 16.623 120.823
CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Divided Measured 779.167 1.78438 1390.33
GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Ranked 65.4586 1.26868 83.0461
LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Squared 6300.2 1.69891 10703.5
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 73561 136638
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] Divided Rooted 27.7254 1.58807 44.0299
TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Subtracted Ranked 350 60 290
WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Measured 24806.9 4437 20369.9
49 ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Divided Ranked 133 1.26667 105
CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Subtracted Measured 24806.9 4437 20369.9
CSTF3 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Squared 201896 69990 131906
DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Ranked 350 60 290
KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Divided Rooted 27.7254 1.58807 44.0299
MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Subtracted 137.446 16.623 120.823
NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Divided Measured 779.167 1.78438 1390.33
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Squared 28994.2 1.69212 17134.8
50 no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted 173408 69581 242989
ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Divided Ranked 133 1.26667 105
CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Squared 28994.2 1.69212 17134.8
CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Subtracted Ranked 350 60 290
CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Measured 24473.9 4346.1 20127.8
KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Divided Rooted 27.7254 1.58807 44.0299
MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Subtracted 137.446 16.623 120.823
NEUROD1 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Divided Measured 779.167 1.78438 1390.33
51 no value hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Subtracted Rooted 137.446 16.623 120.823
CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Ranked 350 60 290
FIP1L1 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Measured 23640.2 4160.4 19479.8
HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Squared 173408 69581 242989
KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Divided Rooted 27.7254 1.58807 44.0299
NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured 779.167 1.78438 1390.33
SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] Ranked 133 1.26667 105
STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Squared 28994.2 1.69212 17134.8
52 AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Ranked 133 1.26667 105
CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Measured 779.167 1.78438 1390.33
CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Subtracted 23422.4 4042.1 19380.3
HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared 173408 69581 242989
MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Rooted 137.446 16.623 120.823
NEURL neuralized-like. [refseq;acc:nm_004210] Divided 27.9107 1.58239 44.1656
RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Subtracted Ranked 350 60 290
VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Divided Squared 28994.2 1.69212 17134.8
53 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 173408 69581 242989
CDK2AP1 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Divided Measured 779.167 1.78438 1390.33
CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Squared 28994.2 1.69212 17134.8
JUNB transcription factor jun-b. [swissprot;acc:p17275] Ranked 201.144 1.26611 158.868
NDN necdin. [swissprot;acc:q99608] Subtracted Rooted 137.446 16.623 120.823
NDUFS4 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Divided 30.8986 1.50369 46.4619

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/