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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene description Hugo Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 375 to 424 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		network_comparison
    		green
    375 dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] POLR3A 242.686 1.09407 265.516
    376 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] DDX56 257.017 1.09395 234.945
    377 dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] POLR1A 242.691 1.09391 265.481
    378 60s ribosomal protein l30. [swissprot;acc:p04645] RPL30 242.593 1.09387 265.365
    379 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] AK2 241.509 1.0938 264.163
    380 suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] no value 242.109 1.09368 264.79
    381 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] TAF7 200.586 1.09357 183.423
    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 1.09328 183.66
    383 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] RBM39 237.862 1.09242 217.739
    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 1.09083 244.236
    385 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] E2F2
    386 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] RPS14 242.238 1.09029 264.11
    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 1.09015 208.756
    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 1.09011 263.62
    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 1.09008 263.615
    393 spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] TXNL4A 225.719 1.09005 207.072
    394 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] DPP9 218.827 1.08948 238.407
    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 1.08945 262.34
    397 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] CCT3 110.689 1.08932 101.613
    398 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] ITGB1BP3 218.818 1.0893 238.358
    399 clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] CLTC 207.889 1.08821 226.226
    400 phosducin-like protein (phlp). [swissprot;acc:q13371] PDCL 207.908 1.08807 226.218
    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 1.0879 226.209
    406 transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] no value 265.634 1.08731 244.304
    407 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] MRPS9 239.75 1.08673 260.544
    408 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] CEBPZ 255.112 1.08649 234.804
    409 rna polymerase i associated factor 53. [refseq;acc:nm_022490] POLR1E 241.045 1.08641 261.874
    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 1.0864 253.539
    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 1.08567 261.416
    413 dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] POLR1C 240.913 1.08525 261.45
    414 katanin p60 subunit a 1. [refseq;acc:nm_007044] KATNA1 232.431 1.08522 252.238
    415 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] KATNB1 232.382 1.08514 252.166
    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 1.08496 261.041
    417 set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] SETMAR 233.539 1.08417 253.197
    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 1.08403 205.9
    422 ras-related protein rab-37. [swissprot;acc:q96ax2] RAB37 240.287 1.08284 260.193
    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

    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/