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 2401 to 2450 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
601 PRKAG2 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Squared 34129.6 40434.5 1.18473
SYMPK symplekin. [swissprot;acc:q92797] Measured 15213.4 13418.1 1.1338
VPS39 vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] Ranked 206.274 218.792 1.06069
WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Rooted 138.032 127.651 1.08132
602 ATXN2L ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] Measured 4864.66 5514.87 1.13366
CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Rooted 138.032 127.651 1.08132
MAP4 microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] Ranked 206.274 218.792 1.06069
TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Squared 19129.8 22652.9 1.18417
603 no value ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Measured 4864.66 5514.87 1.13366
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Squared 34071.5 40336.5 1.18388
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Rooted 60.0742 64.9418 1.08103
LEF1 lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Ranked 225.829 212.945 1.0605
604 no value alpha-nac protein. [sptrembl;acc:q9h009] Squared 34069.4 40333 1.18385
RPL15 60s ribosomal protein l15. [swissprot;acc:p39030] Ranked 217.862 230.978 1.0602
SLU7 step ii splicing factor slu7. [refseq;acc:nm_006425] Rooted 60.0742 64.9418 1.08103
VCL vinculin (metavinculin). [swissprot;acc:p18206] Measured 5958.23 6743.37 1.13177
605 ATP2C2 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 6143.52 6950.75 1.1314
DIRAS1 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Squared 34068.1 40330.8 1.18383
HIST1H2BL histone h2b.c (h2b/c). [swissprot;acc:q99880] Ranked 247.47 233.441 1.0601
ZNF547 sedlin. [swissprot;acc:o14582] Rooted 116.061 125.434 1.08076
606 no value synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
ATP2C1 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Measured 6148.94 6955.76 1.13121
DIRAS2 di-ras2. [refseq;acc:nm_017594] Squared 34068 40330.7 1.18383
HIST2H2BA histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Ranked 247.47 233.441 1.0601
607 no value histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]
CNDP2 cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] Squared 26583.8 31468.6 1.18375
CSTF2T likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Measured 14976.4 13246.6 1.13058
TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Rooted 116.061 125.434 1.08076
608 no value histone h2b. [refseq;acc:nm_175055] Ranked 247.47 233.441 1.0601
FDXR nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] Squared 24560.6 29071.1 1.18365
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] Measured 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
609 no value histone h2b.s (h2b/s). [swissprot;acc:p57053] Ranked 247.47 233.441 1.0601
B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Measured 3886.62 3438.82 1.13022
PEF1 pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Rooted 62.9281 67.99 1.08044
PYCR2 pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Squared 12276.9 14526 1.1832
610 no value histone h2b.d (h2b/d). [swissprot;acc:q99877] Ranked 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
KYNU kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Measured 8430.03 9518.11 1.12907
PYCR1 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Squared 12347.6 14594.8 1.18199
611 no value bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 23487.1 27726.3 1.18049
DYNC1I2 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Measured 5148.71 5811.74 1.12878
HIST3H3 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Ranked 247.47 233.441 1.0601
NAT10 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Rooted 51.0091 55.0909 1.08002
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] Squared 18595.6 21936.3 1.17965
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] Measured 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
613 no value histone h2b.e (h2b/e). [swissprot;acc:q99879] Ranked 247.47 233.441 1.0601
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Measured 3975.77 4485.05 1.1281

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/