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.


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 4908 to 4957 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
307 serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Ranked Divided 1 242.153 266.673 1.10126
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Measured 12365.2 14824.9 1.19892
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Squared Subtracted 0 61.6678 132.922 71.2542
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] Rooted 5.47723 7.07107 1.59384
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Divided 1 50.4687 45.2733 1.11476
308 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Squared 30596.2 38919.9 1.27205
60s ribosomal protein l34. [swissprot;acc:p49207] Ranked 242.153 266.673 1.10126
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Measured Subtracted 11852.9 10773.5 1079.4
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 0 291.639 377.574 85.935
density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Rooted Divided 1 50.4687 45.2733 1.11476
glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] 0 22.112 20.6871 1.06888
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Squared 4748.4 5654.56 1.19083
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Rooted Subtracted 29.6274 31.1837 1.5563
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Ranked Divided 11414.1 12191.8 1.06814
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Subtracted 16321 15577 744
necdin. [swissprot;acc:q99608] 1 88.2482 110.265 22.0168
neurocalcin delta. [swissprot;acc:p29554] Measured Divided 0 702.055 773.218 1.10136
ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Squared Subtracted 1 32991.5 40704.5 7713
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Rooted 65.9938 73.9449 7.9511
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Measured Divided 4977.09 5966.44 1.19878
transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] Squared Subtracted 0 157.095 228.024 70.929
309 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Measured 1 11848.8 10770.3 1078.5
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Squared Divided 28900.8 36762.6 1.27203
dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] 0 32413.7 38271.3 1.18071
histone h2b.d (h2b/d). [swissprot;acc:q99877] Rooted Subtracted 29.6283 31.1839 1.5556
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Ranked Divided 13651 14572 1.06747
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Squared Subtracted 140.822 210.151 69.329
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Ranked 16321 15577 744
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 1 88.2482 110.265 22.0168
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] Measured 0 260.986 346.751 85.765
ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Squared 1 32987.4 40698.5 7711.1
protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Ranked Divided 242.153 266.673 1.10126
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Rooted Subtracted 65.9938 73.9449 7.9511
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Measured Divided 4977.8 5966.14 1.19855
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Rooted 0 30.0555 28.1651 1.06712
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Measured 1890.86 2081.91 1.10104
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Rooted 1 56.185 62.6036 1.11424
310 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Measured Subtracted 7551.8 8630.06 1078.26
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Ranked Divided 0 9328.78 8741.55 1.06718
histone h2b.s (h2b/s). [swissprot;acc:p57053] Rooted Subtracted 29.6311 31.1846 1.5535
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Squared Divided 1 28901.4 36762.1 1.27198
integral membrane protein cii-3b. [sptrembl;acc:o75609] Measured Subtracted 0 2218.63 2304.22 85.59
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Ranked 16321 15577 744
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 1 88.2482 110.265 22.0168
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Squared 0 138.269 68.9705 69.2985
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Rooted Divided 1 95.0526 85.3206 1.11406
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] 0 47.6356 44.6445 1.067
protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Ranked 1 242.153 266.673 1.10126
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Measured 0 4755.32 4320.09 1.10075
ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Squared Subtracted 1 30651.3 38253.3 7602

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/