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 green network_comparison
Results: HTML CSV LaTeX Showing element 2101 to 2150 of 66312 in total
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
Interaction Map
red
green
network_comparison
132 DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Subtracted Measured Low confidence 7030.67 7794.8 764.13
Ranked 203.016 189.965 13.051
FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Divided Measured High confidence 2236.61 2980.35 1.33253
HAT1 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Rooted 44.963 55.0576 1.22451
HPRT1 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Squared Low confidence 65137.2 73946.3 1.13524
MAP2K4 dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] Measured 5948.88 5441.83 1.09318
NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Subtracted Ranked High confidence 229.406 196.695 32.711
PTPRB protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Squared 71062.2 95488.6 24426.4
RBM10 rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] Low confidence 67930.9 60946.6 6984.3
RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Rooted High confidence 144.606 157.824 13.218
TGM1 protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] Divided Low confidence 63.8063 68.4797 1.07324
TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Ranked High confidence 350 290 1.2069
133 no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Subtracted 226.887 194.72 32.167
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Divided Measured Low confidence 7013 7662.77 1.09265
ABRA striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Rooted 65.2217 69.9574 1.07261
ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Subtracted High confidence 144.606 157.824 13.218
BBS9 pth-responsive osteosarcoma b1 protein. [refseq;acc:nm_014451] Divided Squared Low confidence 55849.9 49199.6 1.13517
CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Subtracted Measured High confidence 12798.9 10887.2 1911.7
DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Low confidence 7034.43 7797.14 762.71
Ranked 203.007 189.985 13.022
E2F1 transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Rooted 64.712 69.8815 5.1695
GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Divided Measured High confidence 23421.5 17580.4 1.33225
INADL inad-like protein isoform 3; pdz domain protein (drosophila inad-like); protein associated to tight junctions; pals1-associated tight junction protein; inactivation no after-potential d-like protein. [refseq;acc:nm_005799] Subtracted Squared Low confidence 67882.7 60913.7 6969
OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Divided Rooted High confidence 45.4558 55.5995 1.22316
PROM1 prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Ranked Low confidence 220.268 206.997 1.06411
PRSS16 thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Subtracted Squared High confidence 71062.2 95488.6 24426.4
TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Divided 1182.25 1726.55 1.46039
TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Ranked 350 290 1.2069
134 no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Measured 21785.2 16426.1 1.32626
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Subtracted Ranked 226.884 194.79 32.094
transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] Low confidence 218.36 205.4 12.96
CAPN1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Divided Rooted 64.1512 68.7584 1.07182
CCDC47 gk001 protein. [refseq;acc:nm_020198] Subtracted Squared High confidence 71062.2 95488.6 24426.4
CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Measured 12796.8 10886 1910.8
DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Divided Ranked 350 290 1.2069
DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Subtracted Measured Low confidence 7054.1 7809.38 755.28
E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Rooted 64.712 69.8815 5.1695
GATAD2A p66 alpha. [refseq;acc:nm_017660] Divided Squared High confidence 81888.8 56306.5 1.45434
GSTO2 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Measured Low confidence 6670.21 7286.66 1.09242
MPDZ multiple pdz domain protein. [refseq;acc:nm_003829] Subtracted Squared 67876.4 60909.3 6967.1
NHLH1 helix-loop-helix protein 1 (hen1) (nescient helix loop helix 1) (nscl- 1). [swissprot;acc:q02575] Divided 55838.6 49199.4 1.13494
POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Rooted High confidence 44.849 54.7964 1.2218
SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted 54.8203 67.934 13.1137
TAGLN transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] Divided Ranked Low confidence 218.561 205.431 1.06391
135 AADAT alpha-aminoadipate aminotransferase; l-kynurenine/alpha-aminoadipate aminotransferase; kynurenine aminotransferase ii. [refseq;acc:nm_016228] Subtracted Measured 9986.51 10741.3 754.79
ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Divided High confidence 21785.2 16426.1 1.32626
CACNG8 voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Subtracted Rooted 49.2923 62.3969 13.1046
CAPN2 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Divided Low confidence 64.1536 68.7605 1.07181
CLSTN2 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Subtracted Squared High confidence 71033.4 95440.2 24406.8
CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Divided Ranked 350 290 1.2069

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/