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 4358 to 4407 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
273 dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Ranked Subtracted 1 243.208 266.617 23.409
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Measured Divided 3199.4 3870.8 1.20985
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] Squared 16120.1 20665.7 1.28198
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Rooted Subtracted 0 13.8773 11.824 2.0533
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Divided 1 66.1064 74.1074 1.12103
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Measured Subtracted 5181.2 6410.58 1229.38
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Divided 0 1410.81 1582.65 1.1218
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] Squared Subtracted 1039.56 927.649 111.911
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Rooted 1 57.45 66.332 8.882
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Divided 0 24.598 26.8697 1.09235
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Ranked 12748.1 11770.9 1.08302
274 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] Squared Subtracted 1 30807.7 39351.7 8544
40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] Ranked 0 11977.8 12842.5 864.7
60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Squared Divided 4214.44 5226.4 1.24012
60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Ranked Subtracted 1 242.744 266.07 23.326
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Measured 0 1491.75 1591.6 99.85
brain protein 16. [refseq;acc:nm_016458] Divided 2155.75 2418.14 1.12172
chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 1 3119.98 2579.49 1.20953
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Ranked 0 10432.4 11298.4 1.08301
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Rooted Subtracted 1 57.4586 66.3336 8.875
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Squared 0 274.947 163.071 111.876
grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Rooted Divided 1 66.1063 74.1068 1.12102
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Ranked 241.373 267.352 1.10763
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Squared 16120.1 20665.7 1.28198
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Measured Subtracted 5181.2 6410.58 1229.38
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Rooted Divided 0 32.8979 30.1206 1.09221
transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] Subtracted 6.63325 4.58258 2.05067
275 40s ribosomal protein s5. [swissprot;acc:p46782] Ranked 1 242.473 265.756 23.283
adiponectin receptor 2. [refseq;acc:nm_024551] Rooted 41.8357 50.6469 8.8112
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 0 53.8801 55.9159 2.0358
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Divided 1 66.1048 74.0977 1.12091
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Ranked 241.373 267.352 1.10763
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 0 10783 11674.1 1.08264
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Measured Subtracted 1 10264.9 9043.51 1221.39
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Squared 0 2268.24 2378.75 110.51
pnas-18. [sptrembl;acc:q9bzu3] Divided 14643.9 11814.6 1.23947
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Measured Subtracted 2156.64 2254.12 97.48
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Squared Divided 1 16120.1 20665.7 1.28198
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Measured 3119.98 2579.49 1.20953
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] Ranked Subtracted 0 15977.3 15115.5 861.8
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Squared 1 59331.2 67833.7 8502.5
swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075] Measured Divided 0 717.401 804.725 1.12172
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Rooted 32.8937 30.117 1.0922
276 60s ribosomal protein l32. [swissprot;acc:p02433] Ranked 1 241.13 266.969 1.10716
60s ribosomal protein l9. [swissprot;acc:p32969] 0 10741.6 9922.33 1.08257
Rooted 26.3707 28.8011 1.09216
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Measured 10817.1 12125.1 1.12092
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Squared Subtracted 255.854 146.067 109.787
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Ranked 1 258.437 235.183 23.254
cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Rooted 128.909 120.173 8.736

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/