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 description Gene Hugo Value Type Network Comparison Type red Interaction Map Filtered network_comparison green
    Results: HTML CSV LaTeX Showing element 2725 to 2774 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		Network Comparison Type
    		red
    		network_comparison
    		green
    341 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] PCF11 Rooted Subtracted 120.033 7.128 112.905
    ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] RRM1 Squared Divided 32056.4 1.24673 39965.8
    serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] PPP2CA Measured Subtracted 4916.8 1028.62 3888.18
    ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] UQCRFSL1 Ranked 240.788 20.628 261.416
    342 40s ribosomal protein s20. [swissprot;acc:p17075] RPS20 Divided 243.5 1.09737 267.21
    dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] POLR1C Subtracted 240.913 20.537 261.45
    hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] HGS Squared Divided 70830.5 1.24653 56822
    homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] HOXB5 Measured 20446.1 1.18049 24136.4
    probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] EBNA1BP2 Rooted 49.2715 1.10765 54.5757
    serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] PPP6C Squared Subtracted 31620.5 6630.2 38250.7
    steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] ESRRA Measured 10230.1 1026.1 11256.2
    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 Rooted 46.0352 6.984 53.0192
    343 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] no value Divided 50.3169 1.10749 45.4333
    conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] COG7 Squared 70830.5 1.24653 56822
    homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] HOXA5 Measured 20446.1 1.18049 24136.4
    protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] PRMT3 Ranked 241.625 1.0973 265.136
    rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] GIPC1 Subtracted 231.73 20.478 211.252
    sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] SAPS3 Squared 31620.5 6630.2 38250.7
    transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] E2F2 Rooted 46.0352 6.984 53.0192
    tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] TFIP11 Measured 4991.48 1022.6 6014.08
    344 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] no value Ranked Divided 241.625 1.0973 265.136
    acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] ACACA Squared Subtracted 31597.8 6619.1 38216.9
    ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] no value Rooted 57.9068 6.9494 64.8562
    ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] CANT1 Measured 9921.43 1019.77 10941.2
    dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] POLR1B Ranked 240.6 20.441 261.041
    homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] no value Measured Divided 20446.1 1.18049 24136.4
    isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] IDH2 Squared 37226.9 1.24641 46400.1
    suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] PPAN-P2RY11 Rooted 49.4233 1.10743 54.7327
    345 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] DHX15 56.2615 1.10725 62.2958
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 Measured 20446.1 1.18049 24136.4
    sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] SH3GL1 Squared 35793 1.24592 44595.3
    splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] no value Ranked Subtracted 224.445 20.401 204.044
    u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] SNRPA1 Rooted 57.9068 6.9494 64.8562
    ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] CMPK Ranked Divided 242.14 1.09729 265.697
    vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] SORBS3 Squared Subtracted 29160.4 6409.8 35570.2
    voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] CACNG8 Measured 4068.78 1013.4 5082.18
    346 40s ribosomal protein s3. [swissprot;acc:p23396] RPS3 Ranked Divided 241.612 1.09729 265.119
    apical-like protein (apxl protein). [swissprot;acc:q13796] SHROOM2 Subtracted 231.492 20.356 211.136
    grb2-related adaptor protein. [swissprot;acc:q13588] GRAP Rooted Divided 61.4282 1.10716 68.0107
    importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] CSE1L Squared 34018.3 1.24559 42373
    septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] SEPT1 Measured 14229.2 1.17931 16780.7
    splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] SF3A2 Rooted Subtracted 57.9819 6.9483 64.9302
    vav proto-oncogene. [swissprot;acc:p15498] VAV1 Squared 31223.8 6390.5 37614.3
    voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] CACNG3 Measured 4068.78 1013.4 5082.18
    347 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] TIPRL Rooted Divided 66.4284 1.10713 60.0004
    enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] PRSS7 Measured 4991.02 1.17914 5885.09
    gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] AK3 Ranked 242.14 1.09729 265.697
    krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] KLF5 Rooted Subtracted 57.9819 6.9483 64.9302
    shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] SHROOM3 Ranked 231.481 20.35 211.131
    small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] SNRPD2 Squared Divided 16573.6 1.24522 20637.8

    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/