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 2275 to 2324 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
285 dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Ranked Subtracted 242.691 265.481 22.79
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Measured 4068.56 5252.6 1184.04
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Divided 23326.5 19296.4 1.20885
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Squared Subtracted 32117 40054 7937
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Ranked Divided 224.647 203.242 1.10532
transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Rooted Subtracted 108.653 100.352 8.301
286 60s ribosomal protein l30. [swissprot;acc:p04645] Ranked 242.593 265.365 22.772
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] Divided 224.633 203.251 1.1052
exocyst complex component sec5. [swissprot;acc:q96kp1] Measured 23316 19288.8 1.20878
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Squared Subtracted 32056.4 39965.8 7909.4
rna-binding protein. [refseq;acc:nm_019027] Measured 4069.83 5252.17 1182.34
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Rooted Divided 51.8717 46.3287 1.11965
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Squared 6693.64 8564.94 1.27956
transforming protein n-ras. [swissprot;acc:p01111] Rooted Subtracted 108.65 100.35 8.3
287 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Ranked Divided 240.758 266.079 1.10517
apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Measured Subtracted 4069.83 5252.17 1182.34
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Squared Divided 6693.64 8564.94 1.27956
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Rooted 51.8714 46.3281 1.11965
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Measured 23303.1 19279.5 1.2087
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Ranked Subtracted 225.217 202.459 22.758
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Rooted 97.1967 105.302 8.1053
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Squared 28878.8 36783.5 7904.7
288 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Ranked Divided 240.758 266.078 1.10517
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Measured 23422.4 19380.3 1.20857
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Squared 6693.64 8564.94 1.27956
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Rooted 51.8789 46.3416 1.11949
ns1-associated protein 1. [refseq;acc:nm_006372] Measured Subtracted 4069.83 5252.17 1182.34
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Squared 28896.2 36767 7870.8
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Rooted 55.8956 63.9636 8.068
syntaxin 10 (syn10). [swissprot;acc:o60499] Ranked 234.691 257.442 22.751
289 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Measured 4069.83 5252.17 1182.34
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Ranked Divided 272.781 246.892 1.10486
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Squared 6693.64 8564.94 1.27956
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Rooted 57.4274 64.2609 1.11899
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Subtracted 55.8956 63.9636 8.068
syntaxin 6. [swissprot;acc:o43752] Ranked 234.673 257.414 22.741
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Squared 28896.2 36767 7870.8
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Measured Divided 4682.88 5646.19 1.20571
290 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Squared 15734.4 20126.8 1.27916
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Rooted 75.6323 67.6572 1.11788
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Measured Subtracted 4071.1 5251.75 1180.65
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Squared 28896.2 36767 7870.8
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Ranked Divided 231.969 210.064 1.10428
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Subtracted 242.109 264.79 22.681
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Measured Divided 4991.48 6014.08 1.20487
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Rooted Subtracted 66.1122 74.1438 8.0316
291 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] Ranked 241.509 264.163 22.654
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 251.679 228.037 1.10368
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Measured Subtracted 5894.75 7073.65 1178.9
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Rooted 66.1064 74.1074 8.001

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/