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 564 to 613 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
141 trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Subtracted 0 9411.34 11119.7 1708.36
142 ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Divided 1 59 49 1.20408
thrombospondin 3 precursor. [swissprot;acc:p49746] Subtracted 239.99 269.234 29.244
transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] 0 16614 18296 1682
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Divided 8214.41 7026.41 1.16908
143 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 1 59 49 1.20408
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] 0 11124.8 13005.3 1.16904
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Subtracted 9545 7868 1677
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 1 240.133 211.382 28.751
144 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 239.35 267.915 28.565
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Divided 0 11123.4 13000.1 1.16872
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] 1 265.686 319.651 1.20312
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Subtracted 0 12225.7 13893.1 1667.4
145 lamin b2. [swissprot;acc:q03252] 12135.4 13802 1666.6
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 1 239.336 267.881 28.545
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Divided 265.639 319.546 1.20293
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 0 7955.61 6817.49 1.16694
146 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 12577.8 14662.1 1.16571
kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] 1 265.632 319.531 1.20291
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Subtracted 0 3208.8 4871.6 1662.8
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] 1 239.336 267.879 28.543
147 60s ribosomal protein l7. [swissprot;acc:p18124] Divided 0 11080.3 9505.89 1.16562
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Subtracted 1 239.32 267.842 28.522
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Divided 50.7983 42.3003 1.2009
tubby protein homolog. [swissprot;acc:p50607] Subtracted 0 12303.7 10641.7 1662
148 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 7706.5 6058 1648.5
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] 1 226.582 198.444 28.138
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Divided 296.677 247.559 1.19841
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] 0 6755.71 7863.63 1.164
149 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 1 142 170 1.19718
block 23. [sptrembl;acc:q8nhw5] 0 11469.3 13334.8 1.16265
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] Subtracted 13942.8 15586.4 1643.6
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 1 226.582 198.444 28.138
150 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] 0 7495.26 9130.38 1635.12
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Divided 1 55 46 1.19565
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Subtracted 226.582 198.444 28.138
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] Divided 0 8730 7516 1.16152
151 myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 1 55 46 1.19565
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Subtracted 0 7234.6 8858.94 1624.34
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 1 226.582 198.444 28.138
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Divided 0 7502.08 6461.83 1.16098
152 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 1 55 46 1.19565
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Subtracted 0 12301.4 10680.5 1620.9
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] Divided 11438 13277.1 1.16079
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Subtracted 1 226.582 198.444 28.138
153 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Divided 249.663 298.263 1.19466
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Subtracted 226.582 198.444 28.138
methyltransferase like 2. [refseq;acc:nm_018396] 0 17946 16326 1620
tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] Divided 7879.3 6789.92 1.16044
154 musashi 2 isoform a. [refseq;acc:nm_138962] Subtracted 1 227.491 199.458 28.033

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/