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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
63 phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Measured Subtracted 0 1442 977 465
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared Divided 1.24091 0.365145 3.3984
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Rooted Subtracted 37.9737 31.257 6.7167
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Squared 99229.9 96418.4 2811.5
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] 1 189976 124480 65496
spermatogenesis associated 6. [refseq;acc:nm_019073] Measured 6475.5 10307.5 3832
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] Divided 0 31.1429 56.278 1.80709
Ranked Subtracted 18662.8 15627 3035.8
64 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Rooted Divided 1 63.8686 47.2654 1.35128
amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Measured Subtracted 6475.5 10307.5 3832
ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Ranked 260.532 204.309 56.223
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Squared 0 14470.6 11676.7 2793.9
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 1 144940 81169.7 63770.3
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Measured Divided 4489.19 2765.82 1.6231
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Ranked 266.868 336.159 1.25965
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] Subtracted 0 8152.55 11134.8 2982.25
importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] Measured 607 1068 461
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Squared Divided 1 219048 129762 1.68808
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Rooted Subtracted 137.446 120.823 16.623
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Divided 0 15.7225 22.5496 1.43422
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Measured 0.00001 18 1800000
phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Rooted Subtracted 37.9737 31.257 6.7167
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] Ranked Divided 15264 20387 1.33563
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Squared 50.8715 15.2519 3.33542
65 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 50.642 15.1833 3.33538
60s ribosomal protein l21. [swissprot;acc:p46778] Rooted 20.5734 29.2291 1.42072
cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Measured Subtracted 1 22515.5 18702.6 3812.9
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Ranked Divided 0 7853.67 10406.3 1.32502
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Rooted 1 63.8686 47.2654 1.35128
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Ranked 267.136 336.077 1.25807
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Squared 219048 129762 1.68808
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Rooted Subtracted 137.446 120.823 16.623
metaxin 1. [swissprot;acc:q13505] Squared 0 6149.89 3429.64 2720.25
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 1 144912 81155 63757
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Measured 0 420.365 861.814 441.449
neuralized-like. [refseq;acc:nm_004210] Divided 1 1657.68 2690.25 1.6229
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Ranked Subtracted 0 8519.83 11453 2933.17
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Measured Divided 18 0.00001 1800000
sedlin. [swissprot;acc:o14582] Rooted Subtracted 0 6.55744 6.55744
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] Ranked 1 187.457 243.678 56.221
66 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Measured 17757.5 14008 3749.5
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Squared Divided 0 1797.76 558.241 3.2204
fibrillin 3. [refseq;acc:nm_032447] Measured Subtracted 14246 13809 437
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Rooted Divided 1 63.8686 47.2654 1.35128
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Ranked 267.136 336.077 1.25807
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 0 11461 15180 1.32449
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Squared 1 219048 129762 1.68808
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Subtracted 144911 81154.7 63756.3
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] Ranked 0 9830 6909 2921
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Measured Divided 1 1991.03 3221.38 1.61795

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/