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 Network Comparison Type Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2730 to 2779 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		Value Type
    		description
    		red
    		green
    		network_comparison
    342 EBNA1BP2 Divided Rooted probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 49.2715 54.5757 1.10765
    ESRRA Subtracted Measured steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] 10230.1 11256.2 1026.1
    HGS Divided Squared hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 70830.5 56822 1.24653
    HOXB5 Measured homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 20446.1 24136.4 1.18049
    POLR1C Subtracted Ranked dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 240.913 261.45 20.537
    PPP6C Squared serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] 31620.5 38250.7 6630.2
    RPS20 Divided Ranked 40s ribosomal protein s20. [swissprot;acc:p17075] 243.5 267.21 1.09737
    343 no value Rooted 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 50.3169 45.4333 1.10749
    COG7 Squared conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] 70830.5 56822 1.24653
    E2F2 Subtracted Rooted transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 46.0352 53.0192 6.984
    GIPC1 Ranked rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 231.73 211.252 20.478
    HOXA5 Divided Measured homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 20446.1 24136.4 1.18049
    PRMT3 Ranked protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] 241.625 265.136 1.0973
    SAPS3 Subtracted Squared sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] 31620.5 38250.7 6630.2
    TFIP11 Measured tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 4991.48 6014.08 1022.6
    344 no value Divided homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 20446.1 24136.4 1.18049
    Ranked 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 241.625 265.136 1.0973
    Subtracted Rooted ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 57.9068 64.8562 6.9494
    ACACA Squared acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 31597.8 38216.9 6619.1
    CANT1 Measured ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 9921.43 10941.2 1019.77
    IDH2 Divided Squared isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] 37226.9 46400.1 1.24641
    POLR1B Subtracted Ranked 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 20.441
    PPAN-P2RY11 Divided Rooted suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] 49.4233 54.7327 1.10743
    345 no value Subtracted Ranked splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 224.445 204.044 20.401
    CACNG8 Measured voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 4068.78 5082.18 1013.4
    CMPK Divided Ranked ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] 242.14 265.697 1.09729
    DHX15 Rooted putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] 56.2615 62.2958 1.10725
    HSD17B14 Measured retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 20446.1 24136.4 1.18049
    SH3GL1 Squared 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] 35793 44595.3 1.24592
    SNRPA1 Subtracted Rooted u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 57.9068 64.8562 6.9494
    SORBS3 Squared vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] 29160.4 35570.2 6409.8
    346 CACNG3 Measured voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 4068.78 5082.18 1013.4
    CSE1L Divided Squared importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 34018.3 42373 1.24559
    GRAP Rooted grb2-related adaptor protein. [swissprot;acc:q13588] 61.4282 68.0107 1.10716
    RPS3 Ranked 40s ribosomal protein s3. [swissprot;acc:p23396] 241.612 265.119 1.09729
    SEPT1 Measured septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 14229.2 16780.7 1.17931
    SF3A2 Subtracted Rooted splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] 57.9819 64.9302 6.9483
    SHROOM2 Ranked apical-like protein (apxl protein). [swissprot;acc:q13796] 231.492 211.136 20.356
    VAV1 Squared vav proto-oncogene. [swissprot;acc:p15498] 31223.8 37614.3 6390.5
    347 no value transcription factor btf3 homolog 3. [swissprot;acc:q13892] 34268.1 40650.4 6382.3
    AK3 Divided Ranked gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] 242.14 265.697 1.09729
    CACNG2 Subtracted Measured voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 4068.82 5082.21 1013.39
    KLF5 Rooted 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] 57.9819 64.9302 6.9483
    PRSS7 Divided Measured enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 4991.02 5885.09 1.17914
    SHROOM3 Subtracted Ranked shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] 231.481 211.131 20.35
    SNRPD2 Divided Squared small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 16573.6 20637.8 1.24522
    TIPRL Rooted cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 66.4284 60.0004 1.10713
    348 no value Ranked adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 242.14 265.696 1.09728
    CACNG4 Subtracted Measured voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 4068.91 5082.27 1013.36
    DVL1 Rooted segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 59.0296 65.951 6.9214

    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/