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.


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Value Type Gene description Rank Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2430 to 2479 of 3228 in total
Value Type  : Ranked
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
description
Rank
red
green
network_comparison
rp42 homolog; squamous cell carcinoma-related oncogene. [refseq;acc:nm_020640] 3198 0.00001 0.00001 1
rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] 1624 230.643 227.194 1.01518
runt-related transcription factor 1 (core-binding factor, alpha 2 subunit) (cbf-alpha 2) (acute myeloid leukemia 1 protein) (oncogene aml-1) (polyomavirus enhancer binding protein 2 alpha b subunit) (pebp2-alpha b) (pea2-alpha b) (sl3-3 enhancer factor 1 alpha b subunit) (sl3/akv core-binding factor alpha b subunit). [swissprot;acc:q01196] 2877 0.00001 0.00001 1
runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] 483 237.109 254.667 1.07405
runt-related transcription factor 3 (core-binding factor, alpha 3 subunit) (cbf-alpha 3) (acute myeloid leukemia 2 protein) (oncogene aml-2) (polyomavirus enhancer binding protein 2 alpha c subunit) (pebp2-alpha c) (pea2-alpha c) (sl3-3 enhancer factor 1 alpha c subunit) (sl3/akv core-binding factor alpha c subunit). [swissprot;acc:q13761] 3208 0.00001 0.00001 1
ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265] 1759 219.37 222.086 1.01238
ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [swissprot;acc:q9y230] 2204 219.377 220.8 1.00649
rw1 protein (fragment). [swissprot;acc:q92545] 838 231.734 222.222 1.0428
rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952] 3073 0.00001 0.00001 1
s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] 2647 212.496 212.25 1.00116
s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] 2555 212.953 212.572 1.00179
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] 208 285.684 252.234 1.13261
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] 477 251.926 234.547 1.0741
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 148 296.677 247.559 1.19841
sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] 1387 218.47 213.875 1.02148
sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467] 1377 218.471 213.876
sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] 1378 218.47
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] 1388 218.471
salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [swissprot;acc:p10162] 2716 216.018 215.903 1.00053
sam domain and hd domain-containing protein 1 (dendritic cell-derived ifng-induced protein) (dcip) (monocyte protein 5) (mop-5). [swissprot;acc:q9y3z3] 3124 0.00001 0.00001 1
sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] 1176 218.186 212.672 1.02593
schwannomin interacting protein 1. [refseq;acc:nm_014575] 2900 0.00001 0.00001 1
scratch; scratch 1. [refseq;acc:nm_031309] 1873 210.55 208.305 1.01078
scribble. [refseq;acc:nm_015356] 2528 221.782 222.291 1.0023
scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680] 1575 222.585 218.982 1.01645
sec13-related protein. [swissprot;acc:p55735] 1133 218.484 212.675 1.02731
sec23-interacting protein p125; phospholipase. [refseq;acc:nm_007190] 3097 0.00001 0.00001 1
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] 1644 217.256 214.149 1.01451
secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] 1646
secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] 2453 204.688 205.332 1.00315
secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] 2451 205.333
secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] 2452
secretory pathway component sec31b-1. [refseq;acc:nm_015490] 1143 218.484 212.675 1.02731
sedlin. [swissprot;acc:o14582] 565 129.219 121.261 1.06563
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 513 218.596 204.344 1.06975
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 514 218.613 204.382 1.06963
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 519 218.702 204.582 1.06902
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] 543 222.156 208.201 1.06703
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 540
semaphorin 6b precursor (semaphorin z) (sema z). [swissprot;acc:q9h3t3] 2832 0.00001 0.00001 1
semaphorin 6c precursor (semaphorin y) (sema y). [swissprot;acc:q9h3t2] 2933
semaphorin 6d isoform 3 precursor. [refseq;acc:nm_153617] 2964
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] 503 238.704 255.68 1.07112
sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] 2843 0.00001 0.00001 1
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] 1517 213.267 209.511 1.01793
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 909 142.077 136.846 1.03823
septin 10 isoform 1. [refseq;acc:nm_144710] 737 125.526 119.402 1.05129
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] 829 135.844 130.259 1.04288
septin 6. [swissprot;acc:q14141] 744 126.604 120.463 1.05098
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 743 126.215 120.078 1.05111

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/