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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    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
    		Hugo
    		description
    		red
    		network_comparison
    		green
    380 no value suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] 242.109 1.09368 264.79
    381 TAF7 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] 200.586 1.09357 183.423
    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 1.09328 183.66
    383 RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 237.862 1.09242 217.739
    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 1.09083 244.236
    385 E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
    386 RPS14 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 242.238 1.09029 264.11
    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 1.09015 208.756
    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 1.09011 263.62
    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 1.09008 263.615
    393 TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 225.719 1.09005 207.072
    394 DPP9 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] 218.827 1.08948 238.407
    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 1.08945 262.34
    397 CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 110.689 1.08932 101.613
    398 ITGB1BP3 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 218.818 1.0893 238.358
    399 CLTC clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] 207.889 1.08821 226.226
    400 PDCL phosducin-like protein (phlp). [swissprot;acc:q13371] 207.908 1.08807 226.218
    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 1.0879 226.209
    406 no value transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 265.634 1.08731 244.304
    407 MRPS9 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 239.75 1.08673 260.544
    408 CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 255.112 1.08649 234.804
    409 POLR1E rna polymerase i associated factor 53. [refseq;acc:nm_022490] 241.045 1.08641 261.874
    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 1.0864 253.539
    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 1.08567 261.416
    413 POLR1C dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 240.913 1.08525 261.45
    414 KATNA1 katanin p60 subunit a 1. [refseq;acc:nm_007044] 232.431 1.08522 252.238
    415 KATNB1 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] 232.382 1.08514 252.166
    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 1.08496 261.041
    417 SETMAR set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] 233.539 1.08417 253.197
    418 CLEC4M cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]
    419 FCER2 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]
    420 CD209 cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]
    421 TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 223.202 1.08403 205.9
    422 RAB37 ras-related protein rab-37. [swissprot;acc:q96ax2] 240.287 1.08284 260.193
    423 RAB26 ras-related protein rab-26. [swissprot;acc:q9ulw5]
    424 POLR2C dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]
    425 MAX max protein. [swissprot;acc:p25912] 227.828 1.082 210.561
    426 DCTN5 dynactin 4. [refseq;acc:nm_032486] 233.142 1.08197 252.253
    427 POLR2E dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] 239.977 1.08146 259.525
    428 DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 253.852 1.0811 234.808
    429 POLR3G polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] 239.709 1.08064 259.038

    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/