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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Filtered Value Type green Gene description network_comparison Interaction Map red Rank Network Comparison Type
Results: HTML CSV LaTeX Showing element 501 to 550 of 38536 in total
Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided
green
description
network_comparison
Interaction Map
red
Rank
958.726 keratin associated protein 1.5. [refseq;acc:nm_031957] 1.05539 Low confidence 1011.83 524
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] 525
958.728 keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 526
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] 522
958.732 keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] 1.05538 527
958.745 keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 1.05537 531
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] 532
958.748 keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] 1.05538 1011.84 528
958.749 star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] 529
958.753 similar to peptidylprolyl isomerase a (cyclophilin a); cyclophilin-lc; cyclophilin homolog overexpressed in liver cancer; chromosome 1 amplified sequence 2. [refseq;acc:nm_178230] 1.05537 530
959.463 keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 1.05484 1012.08 536
961.098 scribble. [refseq;acc:nm_015356] 1.00278 High confidence 958.429 484
965.202 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 1.2878 Low confidence 749.494 144
969.022 elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] 1.00304 966.085 810
971.37 dystrophin. [swissprot;acc:p11532] 1.00552 976.734 794
975 lamin-like protein in hindiii repetitive element derived dna, 3' end (fragment). [sptrembl;acc:q14755] 1.5625 624 92
line-1 reverse transcriptase (fragment). [sptrembl;acc:o00172] 93
putative p150. [sptrembl;acc:o00370] 91
rna transcribed from l1 repetitive element (shr4) (fragment). [sptrembl;acc:q9y443] 90
975.647 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 1.12024 High confidence 870.93 277
Low confidence 367
977 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] 1.47595 High confidence 1442 102
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] 101
988.882 dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] 1.06044 1048.65 369
989.438 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] 1.06041 1049.21 370
991.072 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 1.11025 Low confidence 1100.34 391
992.083 60s ribosomal protein l21. [swissprot;acc:p46778] 1.73441 High confidence 572 72
994.275 spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] 1.02465 Low confidence 1018.78 662
1005.42 mitochondrial ribosomal protein l38. [refseq;acc:nm_032478] 1.09699 916.527 411
1006.57 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 1.00558 1012.19 792
1010.2 solute carrier family 4, sodium bicarbonate cotransporter, member 8. [refseq;acc:nm_004858] 1.06023 952.812 498
1011.49 tera protein. [refseq;acc:nm_021238] 1.01291 1024.55 745
1011.67 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 1.37602 1392.08 112
1015.49 scratch; scratch 1. [refseq;acc:nm_031309] 1.00479 1020.35 798
1020.78 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] 1.16449 876.587 315
1020.84 dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] 1.16456 314
1023.76 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] 1.22025 High confidence 1249.24 189
1026.18 glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] 1.19915 1230.54 199
1035.81 60s ribosomal protein l15. [swissprot;acc:p39030] 1.03681 Low confidence 1073.94 599
1036.1 dynamin-like 120 kda protein, mitochondrial precursor (optic atrophy 1 gene protein). [swissprot;acc:o60313] 1.10804 1148.04 393
1049.11 calponin h2, smooth muscle (neutral calponin). [swissprot;acc:q99439] 1.36592 768.061 114
1060 h2a histone family, member j isoform 1. [refseq;acc:nm_018267] 1.05047 1113.5 561
histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001] 559
histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261] 558
histone h2a; h2a histone family, member r. [refseq;acc:nm_170745] 560
1061.23 solute carrier family 12 (potassium/chloride transporters), member 9; cation-chloride cotransporter-interacting protein. [refseq;acc:nm_020246] 1.04494 1108.92 576
1063.6 regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] 1.2107 1287.7 183
1066.67 alpha 2 globin. [refseq;acc:nm_000517] 1.03569 1104.74 602
1067.65 hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096] 1.03559 1105.65 604
1068 importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] 1.75947 High confidence 607 70

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/