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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 368 to 417 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
red
green
network_comparison
368 PUS1 trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] 242.66 265.715 1.09501
369 MRPL12 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 242.159 265.104 1.09475
370 NUDT12 nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]
371 RPS6KC1 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] 186.52 170.42 1.09447
372 no value ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]
373 MRPL11 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 242.37 265.255 1.09442
374 TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 267.208 244.168 1.09436
375 POLR3A dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] 242.686 265.516 1.09407
376 DDX56 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 257.017 234.945 1.09395
377 POLR1A dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] 242.691 265.481 1.09391
378 RPL30 60s ribosomal protein l30. [swissprot;acc:p04645] 242.593 265.365 1.09387
379 AK2 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 241.509 264.163 1.0938
380 no value suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] 242.109 264.79 1.09368
381 TAF7 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] 200.586 183.423 1.09357
382 TAF7L tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] 200.791 183.66 1.09328
383 RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 237.862 217.739 1.09242
384 E2F1 transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] 266.421 244.236 1.09083
385 E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
386 RPS14 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 242.238 264.11 1.09029
387 no value 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
388 small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 227.575 208.756 1.09015
389 SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]
390 MRPL13 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 241.828 263.62 1.09011
391 RPS16 40s ribosomal protein s16. [swissprot;acc:p17008]
392 RPL13A 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] 241.83 263.615 1.09008
393 TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 225.719 207.072 1.09005
394 DPP9 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] 218.827 238.407 1.08948
395 DPP8 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]
396 no value putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 240.801 262.34 1.08945
397 CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 110.689 101.613 1.08932
398 ITGB1BP3 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 218.818 238.358 1.0893
399 CLTC clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] 207.889 226.226 1.08821
400 PDCL phosducin-like protein (phlp). [swissprot;acc:q13371] 207.908 226.218 1.08807
401 RPA1 replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694]
402 RPA2 replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]
403 PDC phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]
404 RAD52 dna repair protein rad52 homolog. [swissprot;acc:p43351]
405 CLTCL1 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 207.931 226.209 1.0879
406 no value transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 265.634 244.304 1.08731
407 MRPS9 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 239.75 260.544 1.08673
408 CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 255.112 234.804 1.08649
409 POLR1E rna polymerase i associated factor 53. [refseq;acc:nm_022490] 241.045 261.874 1.08641
410 no value tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 233.376 253.539 1.0864
411 GTF2H1 tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]
412 UQCRFSL1 ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] 240.788 261.416 1.08567
413 POLR1C dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 240.913 261.45 1.08525
414 KATNA1 katanin p60 subunit a 1. [refseq;acc:nm_007044] 232.431 252.238 1.08522
415 KATNB1 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] 232.382 252.166 1.08514
416 POLR1B dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] 240.6 261.041 1.08496
417 SETMAR set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] 233.539 253.197 1.08417

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
- Hugo is the HGNC identifier if it exists
- 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/