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 3080 to 3129 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
385 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Ranked Divided 266.421 244.236 1.09083
386 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 242.238 264.11 1.09029
40s ribosomal protein s9. [swissprot;acc:p46781] Subtracted 238.986 257.784 18.798
60s ribosomal protein l8. [swissprot;acc:p25120] Measured Divided 4533.74 5279.4 1.16447
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Subtracted 1833.01 892.67 940.34
protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Rooted Divided 50.0513 45.4124 1.10215
scratch; scratch 1. [refseq;acc:nm_031309] Squared 40388.9 49827.5 1.23369
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Rooted Subtracted 86.1101 92.4812 6.3711
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Squared 30286.5 36362 6075.5
387 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Ranked Divided 242.238 264.11 1.09029
60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Rooted 50.3345 45.6718 1.10209
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Subtracted 98.2298 91.8648 6.365
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Ranked 56.6768 75.3531 18.6763
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Squared Divided 15053 18568 1.23351
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Measured Subtracted 1833.01 892.67 940.34
hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Divided 4533.74 5279.4 1.16447
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Squared Subtracted 30286.5 36362 6075.5
388 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Divided 40315.7 49716.4 1.23318
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Ranked Subtracted 56.7244 75.3948 18.6704
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Rooted 58.6096 64.9655 6.3559
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Squared 30286.5 36362 6075.5
pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Measured Divided 4533.74 5279.4 1.16447
serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Rooted 50.3345 45.6718 1.10209
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Ranked 227.575 208.756 1.09015
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Measured Subtracted 6252.58 7192.88 940.3
389 60s ribosomal protein l34. [swissprot;acc:p49207] Rooted Divided 50.3345 45.6718 1.10209
adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Squared Subtracted 26819.1 32855.4 6036.3
arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] Divided 31819.7 39222.2 1.23264
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Ranked Subtracted 56.7252 75.3954 18.6702
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Rooted 58.4926 64.8047 6.3121
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Measured Divided 4533.74 5279.4 1.16447
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Subtracted 6252.58 7192.88 940.3
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Ranked Divided 227.575 208.756 1.09015
390 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 241.828 263.62 1.09011
adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Squared Subtracted 26822.2 32858.1 6035.9
brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Measured 6252.27 7192.51 940.24
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Ranked 56.7841 75.447 18.6629
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Squared Divided 28895.6 35572.8 1.23108
protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Rooted 50.3345 45.6718 1.10209
rw1 protein (fragment). [swissprot;acc:q92545] Measured 4533.74 5279.4 1.16447
vav proto-oncogene. [swissprot;acc:p15498] Rooted Subtracted 66.0892 72.3741 6.2849
391 40s ribosomal protein s16. [swissprot;acc:p17008] Ranked Divided 241.828 263.62 1.09011
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Squared Subtracted 33384.2 39324.9 5940.7
importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] Divided 28895.6 35572.8 1.23108
pnas-18. [sptrembl;acc:q9bzu3] Rooted Subtracted 97.8205 91.5467 6.2738
protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Divided 50.3345 45.6718 1.10209
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Measured Subtracted 6251.99 7192.17 940.18
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Ranked 225.719 207.072 18.647
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Measured Divided 3658.76 3144.39 1.16358
392 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Ranked 241.83 263.615 1.09008

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/