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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4858 to 4907 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
608 DYNLL2 dynein light chain 2. [refseq;acc:nm_080677] Ranked Subtracted 216.731 229.549 12.818
FDXR nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] Squared Divided 24560.6 29071.1 1.18365
FLNB filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Subtracted 16120.1 20665.7 4545.6
FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Measured 2234.68 2978.53 743.85
NFYB nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Divided 4510.61 5098.74 1.13039
SFRS11 splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] Rooted 59.6517 64.4642 1.08068
Subtracted 4.8125
609 no value dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Ranked 226.523 213.786 12.737
histone h2b.s (h2b/s). [swissprot;acc:p57053] Divided 247.47 233.441 1.0601
AGPAT2 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] Rooted Subtracted 74.3877 79.1931 4.8054
B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Measured Divided 3886.62 3438.82 1.13022
FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Subtracted 2234.73 2978.57 743.84
PEF1 pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Rooted Divided 62.9281 67.99 1.08044
PYCR2 pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Squared 12276.9 14526 1.1832
REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Subtracted 16120.1 20665.7 4545.6
610 no value 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Rooted 74.3557 79.1513 4.7956
histone h2b.d (h2b/d). [swissprot;acc:q99877] Ranked Divided 247.47 233.441 1.0601
CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Rooted 136.706 126.565 1.08012
FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Measured Subtracted 2236.61 2980.35 743.74
KYNU kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Divided 8430.03 9518.11 1.12907
PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Squared Subtracted 16120.1 20665.7 4545.6
PYCR1 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Divided 12347.6 14594.8 1.18199
SOS1 son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Ranked Subtracted 205.74 193.021 12.719
611 no value bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] Squared Divided 23487.1 27726.3 1.18049
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Ranked Subtracted 228.986 216.276 12.71
DYNC1I2 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Measured Divided 5148.71 5811.74 1.12878
ESRRA steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Rooted Subtracted 82.1645 86.9566 4.7921
FBLN2 fibulin-2 precursor. [swissprot;acc:p98095] Measured 8670.59 9412.9 742.31
HIST3H3 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Ranked Divided 247.47 233.441 1.0601
NAT10 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Rooted 51.0091 55.0909 1.08002
PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Squared Subtracted 16120.1 20665.7 4545.6
612 no value u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Divided 18595.6 21936.3 1.17965
AKT1 rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Rooted Subtracted 50.2317 55.0025 4.7708
CBS cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Measured 5480.24 6222.04 741.8
EIF3I eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] Divided 3975.77 4485.05 1.1281
HIST1H2BA testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Ranked 247.47 233.441 1.0601
MYCL1 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Rooted 57.1949 61.7633 1.07987
SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Squared Subtracted 16120.1 20665.7 4545.6
SOS2 son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Ranked 205.89 193.183 12.707
613 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Squared 16120.1 20665.7 4545.6
histone h2b.e (h2b/e). [swissprot;acc:q99879] Ranked Divided 247.47 233.441 1.0601
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Measured 3975.77 4485.05 1.1281
AKT3 rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] Rooted Subtracted 50.2317 55.0025 4.7708
ARD1A n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Squared Divided 17550.2 20701.1 1.17954
MYCN n-myc proto-oncogene protein. [swissprot;acc:p04198] Rooted 57.1971 61.7626 1.07982
NOL5A nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Ranked Subtracted 247.769 235.074 12.695
RHOC transforming protein rhoc (h9). [swissprot;acc:p08134] Measured 5480.24 6222.04 741.8
614 AKT2 rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] Rooted 50.2317 55.0025 4.7708
COPB2 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Squared Divided 51527.6 43689.1 1.17942
GABPA ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Rooted 57.2007 61.7615 1.07973

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/