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.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5708 to 5757 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
357 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Squared Subtracted 0 31.36 0 31.36
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Ranked 1 94 114 20
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Measured 4977.09 5966.44 989.35
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Rooted 46.3291 53.1063 6.7772
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Squared Divided 9811.86 7908.29 1.24071
358 3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] Rooted Subtracted 0 43.8864 44.9836 1.0972
5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Squared 1 34129.6 40434.5 6304.9
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Ranked 0 11869.9 12402.7 532.8
high mobility group protein 1 (hmg-1). [swissprot;acc:p09429] Measured 22962 22910.9 51.1
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided 48 51 1.0625
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Ranked 16321 15577 1.04776
Squared 0.545325 0.615621 1.12891
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Measured 1 5061.11 5950.22 1.17567
nanos (fragment). [sptrembl;acc:q8wy41] Squared Subtracted 0 33.64 5.39669 28.2433
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Rooted 1 51.6736 58.4422 6.7686
ras-related protein rab-37. [swissprot;acc:q96ax2] Ranked 240.287 260.193 19.906
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Divided 243.12 266.662 1.09683
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Measured Subtracted 4977.8 5966.14 988.34
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Squared Divided 9811.73 7908.13 1.24071
serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Rooted 61.2684 67.755 1.10587
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 0 39.7617 37.9899 1.04664
359 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Squared Subtracted 1 34129.4 40434.2 6304.8
60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Ranked Divided 239.277 262.434 1.09678
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Measured Subtracted 0 525 576 51
Rooted 22.9129 24 1.0871
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Measured Divided 1 12798.9 10887.2 1.17559
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Rooted 0 82.3645 86.1594 1.04607
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Measured 48 51 1.0625
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Ranked 16321 15577 1.04776
Squared 0.545325 0.615621 1.12891
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Subtracted 98.1677 70.141 28.0267
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Measured 1 1920.75 2907.43 986.68
pescadillo homolog 1. [swissprot;acc:o00541] Rooted Divided 49.2488 54.4603 1.10582
ras-related protein rab-26. [swissprot;acc:q9ulw5] Ranked Subtracted 240.287 260.193 19.906
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Squared Divided 9812.34 7908.87 1.24068
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Ranked Subtracted 0 8021.78 7496.8 524.98
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Rooted 1 57.6823 64.4212 6.7389
360 60s ribosomal protein l12. [swissprot;acc:p30050] Divided 0 27.5183 28.7547 1.04493
adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] Subtracted 17.9172 16.833 1.0842
alpha-nac protein. [sptrembl;acc:q9h009] Ranked 14204.4 14724.5 520.1
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Rooted 1 46.901 53.624 6.723
dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] Ranked 240.287 260.193 19.906
g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Measured Divided 12796.8 10886 1.17553
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Subtracted 0 348.823 399.534 50.711
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Ranked Divided 16321 15577 1.04776
Squared 0.545325 0.615621 1.12891
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Measured 48 51 1.0625
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Squared Subtracted 98.1677 70.141 28.0267
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Rooted Divided 1 49.3771 54.5905 1.10558
protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Ranked 243.072 266.559 1.09663

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
- 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/