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.


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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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 380 to 429 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
red
green
network_comparison
48 LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Divided 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] Divided Rooted 27.7254 44.0299 1.58807
TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Subtracted Ranked 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] Divided Ranked 133 105 1.26667
CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Subtracted Measured 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] Divided Rooted 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] Divided Measured 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] Divided Ranked 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] Subtracted Ranked 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] Divided Rooted 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] Divided Measured 779.167 1390.33 1.78438
51 no value hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Subtracted Rooted 137.446 120.823 16.623
CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Ranked 350 290 60
FIP1L1 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Measured 23640.2 19479.8 4160.4
HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Squared 173408 242989 69581
KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Divided Rooted 27.7254 44.0299 1.58807
NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured 779.167 1390.33 1.78438
SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] Ranked 133 105 1.26667
STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Squared 28994.2 17134.8 1.69212
52 AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Ranked 133 105 1.26667
CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Measured 779.167 1390.33 1.78438
CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Subtracted 23422.4 19380.3 4042.1
HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared 173408 242989 69581
MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Rooted 137.446 120.823 16.623
NEURL neuralized-like. [refseq;acc:nm_004210] Divided 27.9107 44.1656 1.58239
RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Subtracted Ranked 350 290 60
VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Divided Squared 28994.2 17134.8 1.69212
53 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 173408 242989 69581
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 1390.33 1.78438
CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Squared 28994.2 17134.8 1.69212
JUNB transcription factor jun-b. [swissprot;acc:p17275] Ranked 201.144 158.868 1.26611
NDN necdin. [swissprot;acc:q99608] Subtracted Rooted 137.446 120.823 16.623
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 46.4619 1.50369
Subtracted Ranked 318.982 259.004 59.978
PAPOLA poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Measured 23326.5 19296.4 4030.1
54 DTX2 deltex 2. [refseq;acc:nm_020892] Divided 1618.84 2651.88 1.63814
EXOC2 exocyst complex component sec5. [swissprot;acc:q96kp1] Subtracted 23316 19288.8 4027.2
GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Ranked 185.678 245.247 59.569
HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Squared 173408 242989 69581
JUND transcription factor jun-d. [swissprot;acc:p17535] Divided Ranked 200.941 158.941 1.26425

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/