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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4808 to 4857 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
601 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Rooted Divided 138.032 127.651 1.08132
602 44050 protein. [refseq;acc:nm_178832] Subtracted 108.34 103.501 4.839
ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] Measured Divided 4864.66 5514.87 1.13366
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Rooted 138.032 127.651 1.08132
creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277] Squared Subtracted 58521.9 53975.7 4546.2
microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] Ranked Divided 206.274 218.792 1.06069
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Subtracted 207.26 194.346 12.914
pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Measured 4533.74 5279.4 745.66
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Squared Divided 19129.8 22652.9 1.18417
603 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Measured 4864.66 5514.87 1.13366
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Ranked Subtracted 207.27 194.368 12.902
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Divided 225.829 212.945 1.0605
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Squared 34071.5 40336.5 1.18388
nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Rooted Subtracted 108.34 103.501 4.839
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Measured 4533.74 5279.4 745.66
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Squared 29830.2 34375.9 4545.7
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Rooted Divided 60.0742 64.9418 1.08103
604 60s ribosomal protein l15. [swissprot;acc:p39030] Ranked 217.862 230.978 1.0602
alpha-nac protein. [sptrembl;acc:q9h009] Squared 34069.4 40333 1.18385
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Subtracted 29830.2 34375.9 4545.7
heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Rooted 82.2821 87.1197 4.8376
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Ranked 207.272 194.371 12.901
rw1 protein (fragment). [swissprot;acc:q92545] Measured 4533.74 5279.4 745.66
step ii splicing factor slu7. [refseq;acc:nm_006425] Rooted Divided 60.0742 64.9418 1.08103
vinculin (metavinculin). [swissprot;acc:p18206] Measured 5958.23 6743.37 1.13177
605 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Rooted Subtracted 82.2706 87.1037 4.8331
histone h2b.c (h2b/c). [swissprot;acc:q99880] Ranked Divided 247.47 233.441 1.0601
inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Squared Subtracted 29830.2 34375.9 4545.7
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Ranked 225.829 212.945 12.884
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Measured Divided 6143.52 6950.75 1.1314
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Subtracted 6079.26 6824.47 745.21
sedlin. [swissprot;acc:o14582] Rooted Divided 116.061 125.434 1.08076
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Squared 34068.1 40330.8 1.18383
606 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Rooted Subtracted 50.7801 45.9472 4.8329
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 Divided 6148.94 6955.76 1.13121
di-ras2. [refseq;acc:nm_017594] Squared 34068 40330.7 1.18383
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Ranked 247.47 233.441 1.0601
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Subtracted 207.309 194.452 12.857
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Squared 29830.2 34375.9 4545.7
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Rooted Divided 116.061 125.434 1.08076
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] Measured Subtracted 10231.8 9487.34 744.46
607 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Rooted 50.7803 45.9477 4.8326
bet3 homolog. [swissprot;acc:o43617] Divided 116.061 125.434 1.08076
cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] Squared 26583.8 31468.6 1.18375
double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] Measured Subtracted 10231.8 9487.34 744.46
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Ranked Divided 247.47 233.441 1.0601
inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Squared Subtracted 29830.2 34375.9 4545.7
likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Measured Divided 14976.4 13246.6 1.13058
short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] Ranked Subtracted 216.731 229.549 12.818
608 dynein light chain 2. [refseq;acc:nm_080677]

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
- 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/