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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 380 to 429 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
red
green
network_comparison
380 suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] no value 242.109 264.79 1.09368
381 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] TAF7 200.586 183.423 1.09357
382 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] TAF7L 200.791 183.66 1.09328
383 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] RBM39 237.862 217.739 1.09242
384 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] E2F1 266.421 244.236 1.09083
385 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] E2F2
386 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] RPS14 242.238 264.11 1.09029
387 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] no value
388 small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 227.575 208.756 1.09015
389 small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] SNRPF
390 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] MRPL13 241.828 263.62 1.09011
391 40s ribosomal protein s16. [swissprot;acc:p17008] RPS16
392 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] RPL13A 241.83 263.615 1.09008
393 spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] TXNL4A 225.719 207.072 1.09005
394 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] DPP9 218.827 238.407 1.08948
395 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] DPP8
396 putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] no value 240.801 262.34 1.08945
397 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] CCT3 110.689 101.613 1.08932
398 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] ITGB1BP3 218.818 238.358 1.0893
399 clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] CLTC 207.889 226.226 1.08821
400 phosducin-like protein (phlp). [swissprot;acc:q13371] PDCL 207.908 226.218 1.08807
401 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] RPA1
402 replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] RPA2
403 phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] PDC
404 dna repair protein rad52 homolog. [swissprot;acc:p43351] RAD52
405 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] CLTCL1 207.931 226.209 1.0879
406 transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] no value 265.634 244.304 1.08731
407 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] MRPS9 239.75 260.544 1.08673
408 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] CEBPZ 255.112 234.804 1.08649
409 rna polymerase i associated factor 53. [refseq;acc:nm_022490] POLR1E 241.045 261.874 1.08641
410 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] no value 233.376 253.539 1.0864
411 tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] GTF2H1
412 ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] UQCRFSL1 240.788 261.416 1.08567
413 dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] POLR1C 240.913 261.45 1.08525
414 katanin p60 subunit a 1. [refseq;acc:nm_007044] KATNA1 232.431 252.238 1.08522
415 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] KATNB1 232.382 252.166 1.08514
416 dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] POLR1B 240.6 261.041 1.08496
417 set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] SETMAR 233.539 253.197 1.08417
418 cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] CLEC4M
419 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] FCER2
420 cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] CD209
421 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] TFIP11 223.202 205.9 1.08403
422 ras-related protein rab-37. [swissprot;acc:q96ax2] RAB37 240.287 260.193 1.08284
423 ras-related protein rab-26. [swissprot;acc:q9ulw5] RAB26
424 dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] POLR2C
425 max protein. [swissprot;acc:p25912] MAX 227.828 210.561 1.082
426 dynactin 4. [refseq;acc:nm_032486] DCTN5 233.142 252.253 1.08197
427 dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] POLR2E 239.977 259.525 1.08146
428 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] DDX54 253.852 234.808 1.0811
429 polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] POLR3G 239.709 259.038 1.08064

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/