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 [...,...].
    description Rank Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2858 to 2907 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    transcription factor btf3 homolog 3. [swissprot;acc:q13892] 870 no value 211.908 203.832 1.03962
    transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] 1192 TFCP2 220.742 215.237 1.02558
    transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 406 no value 265.634 244.304 1.08731
    transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 374 TFDP2 267.208 244.168 1.09436
    transcription factor e2-alpha (immunoglobulin enhancer binding factor e12/e47) (transcription factor-3) (tcf-3) (immunoglobulin transcription factor-1) (transcription factor itf-1) (kappa-e2-binding factor). [swissprot;acc:p15923] 3182 TCF3 0.00001 0.00001 1
    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] 384 E2F1 266.421 244.236 1.09083
    transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 385 E2F2
    transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] 666 HES1 229.072 216.576 1.0577
    transcription factor iib. [refseq;acc:nm_013242] 823 C16orf80 206.068 197.471 1.04354
    transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] 2486 GTF3A 218.093 218.72 1.00287
    transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 478 BRF1 228.051 212.321 1.07409
    transcription factor jun-b. [swissprot;acc:p17275] 53 JUNB 201.144 158.868 1.26611
    transcription factor jun-d. [swissprot;acc:p17535] 54 JUND 200.941 158.941 1.26425
    transcription factor lbx1. [swissprot;acc:p52954] 157 LBX1 249.663 298.263 1.19466
    transcription factor maf (proto-oncogene c-maf). [swissprot;acc:o75444] 2792 MAF 0.00001 0.00001 1
    transcription factor mafb (v-maf musculoaponeurotic fibrosarcoma oncogene homolog b). [swissprot;acc:q9y5q3] 2790 no value
    transcription factor maff (v-maf musculoaponeurotic fibrosarcoma oncogene homolog f) (u-maf). [swissprot;acc:q9ulx9] 2737 MAFF 198.278 198.321 1.00022
    transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] 2736 no value
    transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] 2738
    transcription factor mammalian mafa (pancreatic beta-cell specific transcriptional activator). [sptrembl;acc:q8nhw3] 2778 MAFA 0.00001 0.00001 1
    transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206] 2614 RELA 202.821 202.54 1.00139
    transcription factor relb (i-rel). [swissprot;acc:q01201] 2615 RELB
    transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] 1499 DCP1A 224.509 220.411 1.01859
    transcription factor-like protein 4 (max-like bhlhzip protein) (bigmax protein) (mlx). [swissprot;acc:q9uh92] 3091 MLX 0.00001 0.00001 1
    transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] 1664 no value 228.484 231.74 1.01425
    transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8] 1688 MORF4L1 228.523 231.703 1.01392
    transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014] 1662 MORF4L2 228.477 231.747 1.01431
    transcription initiation factor iia alpha and beta chains (tfiia p35 and p19 subunits) (tfiia-42) (tfiial). [swissprot;acc:p52655] 2848 GTF2A1 0.00001 0.00001 1
    transcription initiation factor iia gamma chain (tfiia p12 subunit) (tfiia-12) (tfiias) (tfiia-gamma). [swissprot;acc:p52657] 2946 GTF2A2
    transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] 1620 GTF2B 228.611 225.185 1.01521
    transcription initiation factor iie, alpha subunit (tfiie-alpha) (general transcription factor iie 56 kda subunit). [swissprot;acc:p29083] 2894 GTF2E1 0.00001 0.00001 1
    transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] 3178 no value
    transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269] 1736 GTF2F1 221.921 219.081 1.01296
    transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [swissprot;acc:q15542] 2598 TAF5 202.142 202.436 1.00145
    transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750] 2941 TAF4B 0.00001 0.00001 1
    transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] 2999 TAF4
    transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] 2572 TAF12 203.953 204.285 1.00163
    transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544] 1712 TAF11 208.598 211.375 1.01331
    transcription initiation factor tfiid 30 kda subunit (tafii-30) (tafii30). [swissprot;acc:q12962] 2839 TAF10 0.00001 0.00001 1
    transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594] 2741 TAF9 198.278 198.321 1.00022
    transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] 381 TAF7 200.586 183.423 1.09357
    transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] 2442 TAF6 204.419 203.748 1.00329
    transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] 1561 GATAD2B 167.687 170.455 1.01651
    transcription termination factor, rna polymerase ii; lodestar protein. [refseq;acc:nm_003594] 3043 TTF2 0.00001 0.00001 1
    transcriptional adapter 2-like (ada2-like protein) (kl04p). [swissprot;acc:o75478] 2746 TADA2L 201.476 201.514 1.00019
    transcriptional adaptor 3-like isoform a. [refseq;acc:nm_006354] 2744 TADA3L
    transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472] 1991 WWTR1 219.26 217.194 1.00951
    transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] 266 SIN3A 241.07 267.88 1.11121
    transcriptional coactivator tubedown-100 isoform 1; putative n-acetyltransferase; gastric cancer antigen ga19. [refseq;acc:nm_057175] 2854 NARG1 0.00001 0.00001 1
    transcriptional repressor nac1. [refseq;acc:nm_052876] 2872 BTBD14B

    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/