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 2758 to 2807 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
173 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Rooted Subtracted 0 28.4183 31.4149 2.9966
mesoderm induction early response 1. [refseq;acc:nm_020948] Measured 1914.5 1723.5 191
methyltransferase like 2. [refseq;acc:nm_018396] Squared 1 71576.8 56326.7 15250.1
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Ranked 0 4338.65 5700.79 1362.14
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Rooted 1 37.3005 48.4141 11.1136
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Squared 0 4339.93 3865.57 474.36
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Divided 1 82624.3 115061 1.39258
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Ranked Subtracted 201.515 228.752 27.237
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Divided 227.032 193.056 1.17599
suppressor of actin 1. [refseq;acc:nm_014016] 0 19088.1 16804.6 1.13589
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Measured Subtracted 1 4556.79 2945.28 1611.51
174 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Rooted 0 23.1768 26.17 2.9932
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Divided 15.8745 18.303 1.15298
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Squared 48.3438 75.3968 1.5596
cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Subtracted 1 71576.8 56326.7 15250.1
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Ranked Divided 335 286 1.17133
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Measured 0 488.43 612.604 1.25423
kappa b-ras 1. [refseq;acc:nm_020345] Ranked Subtracted 12657.7 11299.1 1358.6
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Squared 58677.8 58207.8 470
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Ranked 1 228.1 200.968 27.132
mad protein (max dimerizer). [swissprot;acc:q05195] Measured Divided 4455.95 5774.03 1.2958
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Rooted 145.551 168.796 1.1597
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Ranked 0 13248.5 11666.4 1.13561
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Rooted Subtracted 1 37.3005 48.4141 11.1136
sedlin. [swissprot;acc:o14582] Squared Divided 112820 157033 1.39189
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] Measured Subtracted 4556.83 2945.38 1611.45
uridine kinase-like 1. [swissprot;acc:q9nwz5] 0 633.433 821.711 188.278
175 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Ranked Divided 1 199.949 234.187 1.17123
cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Measured 0 1382.5 1107 1.24887
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Squared 48.5538 75.7214 1.55954
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Rooted Subtracted 1 37.3005 48.4141 11.1136
fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Squared 71576.8 56326.7 15250.1
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Measured 0 2056.14 2244.06 187.92
keratin associated protein 9.2. [refseq;acc:nm_031961] Squared 3693.52 3232.47 461.05
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Ranked 1 228.085 201.006 27.079
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Measured Divided 4456.67 5773.77 1.29553
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Rooted 0 61.6393 70.9983 1.15183
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Subtracted 47.6356 44.6445 2.9911
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Divided 1 145.551 168.796 1.1597
putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] Ranked Subtracted 0 11573.8 10231.3 1342.5
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Measured 1 4556.99 2945.8 1611.19
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Squared Divided 112820 157033 1.39189
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Ranked 0 13248.5 11666.4 1.13561
176 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Subtracted 11935.1 10592.8 1342.3
40s ribosomal protein s29. [swissprot;acc:p30054] Measured 1711.6 1895.38 183.78
bet3 homolog. [swissprot;acc:o43617] Squared Divided 1 112820 157033 1.39189
cullin homolog 2 (cul-2). [swissprot;acc:q13617] Rooted Subtracted 37.3005 48.4141 11.1136
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Squared Divided 0 48.5538 75.7214 1.55954
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Ranked 13068 11528 1.13359
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Rooted 20.3469 17.7078 1.14904

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/