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 1132 to 1181 of 7460 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
283 transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Subtracted 0 197.333 290.667 93.334
284 60s ribosomal protein l15. [swissprot;acc:p39030] 846.216 753.793 92.423
60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Divided 1753.85 1956.36 1.11547
paxillin. [swissprot;acc:p49023] 1 5221.28 6314.35 1.20935
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Subtracted 677.5 1865.5 1188
285 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Divided 0 2698.62 3010.22 1.11547
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Subtracted 1 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
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Subtracted 0 5699.32 5607.7 91.62
286 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Divided 5497.01 6127.24 1.11465
exocyst complex component sec5. [swissprot;acc:q96kp1] 1 23316 19288.8 1.20878
rna-binding protein. [refseq;acc:nm_019027] Subtracted 4069.83 5252.17 1182.34
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] 0 939 848 91
287 5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] Divided 726.245 808.929 1.11385
apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Subtracted 1 4069.83 5252.17 1182.34
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Divided 23303.1 19279.5 1.2087
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Subtracted 0 2363.32 2454.04 90.72
288 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Divided 1 23422.4 19380.3 1.20857
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 0 1293.73 1161.64 1.11371
ns1-associated protein 1. [refseq;acc:nm_006372] Subtracted 1 4069.83 5252.17 1182.34
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] 0 1631.97 1542.23 89.74
289 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 1 4069.83 5252.17 1182.34
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 0 89 89
tubby protein homolog. [swissprot;acc:p50607] Divided 3797.57 4228.27 1.11341
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 1 4682.88 5646.19 1.20571
290 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] 0 1370.82 1525.56 1.11288
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Subtracted 1 4071.1 5251.75 1180.65
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0 0 89 89
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Divided 1 4991.48 6014.08 1.20487
291 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted 0 0 89 89
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 1 5894.75 7073.65 1178.9
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Divided 44490.5 36927.5 1.20481
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] 0 1961.09 2179.77 1.11151
292 ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] 11223 12473 1.11138
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] 1 4641.09 5588.75 1.20419
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Subtracted 950.561 2108.52 1157.96
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 0 952.488 863.886 88.602
293 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 764.479 676.971 87.508
block 23. [sptrembl;acc:q8nhw5] Divided 1943.32 2159.55 1.11127
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] 1 4641.09 5588.75 1.20419
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Subtracted 4512.19 5655.52 1143.33
294 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Divided 22515.5 18702.6 1.20387
lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] Subtracted 0 841.301 753.849 87.452
mesoderm induction early response 1. [refseq;acc:nm_020948] Divided 1914.5 1723.5 1.11082
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Subtracted 1 4512.19 5655.52 1143.33
295 adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] Divided 0 426.8 384.843 1.10902
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Subtracted 1 5720.25 4577.5 1142.75
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Divided 13261.9 11017.8 1.20368
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] Subtracted 0 717.401 804.725 87.324
296 histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 2131.42 2218.51 87.09

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/