MK5 Microarray Data

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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.

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	measured	expected	final	Hugo

Results: HTML CSV LaTeX

Showing element 1 to 50 of 350 in total

Hugo  : no value

Rank	description	measured	expected	final
4		3.66001	3.3348	1.097520091
17		0.0856348	0.180231	0.475139127
28	DOK-LIKE PROTEIN. [RefSeq;Acc:NM_024872]	0.0753031	0.176719	0.426117735
32	PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC (EC 2.7.1.112) (P60-SRC) (C-SRC). [SWISSPROT;Acc:P12931]	0.141847	0.33698	0.420935961
53	DISKS LARGE-ASSOCIATED PROTEIN 2 (DAP-2) (SAP90/PSD-95-ASSOCIATED PROTEIN 2) (SAPAP2) (PSD-95/SAP90 BINDING PROTEIN 2) (FRAGMENT). [SWISSPROT;Acc:Q9P1A6]	0.318849	0.775495	0.411155456
55		0.231369	0.562729	0.411155281
58	"DJ681N20.2 (NOVEL PROTEIN SIMILAR TO FERRITIN, LIGHT POLYPEPTIDE (FTL)). [SPTREMBL;Acc:Q9BYW6]"	0.0511645	0.124441	0.411154684
61	PUTATIVE ADENOSYLHOMOCYSTEINASE 3 (EC 3.3.1.1) (S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:Q96HN2]	0.312681	0.760495	0.411154577
78	ASPARTATE BETA-HYDROXYLASE ISOFORM B; JUNCTIN ISOFORM 1; JUNCTATE; ASPARTYL/ASPARAGINYL-BETA-HYDROXYLASE; PEPTIDE-ASPARTATE BETA-DIOXYGENASE; HUMBUG. [RefSeq;Acc:NM_032468]	0.06383	0.157168	0.406125929
85	TRANSCRIPTION FACTOR DP-1 (E2F DIMERIZATION PARTNER 1) (DRTF1- POLYPEPTIDE-1) (DRTF1). [SWISSPROT;Acc:Q14186]	0.788778	2.02915	0.388723357
89		0.152828	0.396725	0.385224022
92		0.914796	2.37847	0.38461532
126	UBA/UBX 33.3 KDA PROTEIN. [SWISSPROT;Acc:Q04323]	0.375086	1.05643	0.3550505
127	ERO1-LIKE. [RefSeq;Acc:NM_014584]	0.0588477	0.165745	0.355049624
134	INTERLEUKIN-1 RECEPTOR-ASSOCIATED KINASE 4; INTERLEUKIN-1 RECEPTOR ASSOCIATED KINASE 4. [RefSeq;Acc:NM_016123]	0.290469	0.826637	0.351386401
159	FORMIN BINDING PROTEIN 3; FAS-LIGAND ASSOCIATED FACTOR 1; HUNTINGTIN-INTERACTING PROTEIN A; NY-REN-6 ANTIGEN. [RefSeq;Acc:NM_017892]	0.429285	1.22508	0.350413851
160	HUNTINGTIN-INTERACTING PROTEIN HYPA/FBP11 (FRAGMENT). [SPTREMBL;Acc:O75404]	0.40616	1.16002	0.350131894
178	FILAMIN A (ALPHA-FILAMIN) (FILAMIN 1) (ENDOTHELIAL ACTIN-BINDING PROTEIN) (ABP-280) (NONMUSCLE FILAMIN). [SWISSPROT;Acc:P21333]	0.0413389	0.122543	0.337341994
180	TRINUCLEOTIDE REPEAT CONTAINING 15. [RefSeq;Acc:NM_015575]	0.0561104	0.16661	0.336776904
213	RD PROTEIN. [SWISSPROT;Acc:P18615]	0.155654	0.485577	0.320554721
230	JUN DIMERIZATION PROTEIN. [RefSeq;Acc:NM_130469]	0.193648	0.614336	0.315215127
247	TRANSCRIPTION FACTOR BTF3 HOMOLOG 3. [SWISSPROT;Acc:Q13892]	0.625831	2.00343	0.312379769
249	NASCENT-POLYPEPTIDE-ASSOCIATED COMPLEX ALPHA POLYPEPTIDE. [RefSeq;Acc:NM_005594]	0.804734	2.57998	0.311914821
250	ALPHA-NAC PROTEIN. [SPTREMBL;Acc:Q9H009]	0.755644	2.42272	0.311899023
251		0.743299	2.38318	0.311893772
261	APOBEC-1 COMPLEMENTATION FACTOR ISOFORM 1; APOBEC-1 STIMULATING PROTEIN; APO-B RNA EDITING PROTEIN. [RefSeq;Acc:NM_014576]	0.0555455	0.180015	0.308560398
262		0.0556846	0.180466	0.308560061
263	RNA-BINDING PROTEIN. [RefSeq;Acc:NM_019027]	0.0560669	0.181705	0.308560029
267		0.152054	0.494121	0.307726245
269	SPLICING FACTOR 3B SUBUNIT 3 (SPLICEOSOME ASSOCIATED PROTEIN 130) (SAP 130) (SF3B130) (PRE-MRNA SPLICING FACTOR SF3B 130 KDA SUBUNIT). [SWISSPROT;Acc:Q15393]	1.08194	3.53138	0.306378809
287	"FATTY ACID-BINDING PROTEIN, EPIDERMAL (E-FABP) (PSORIASIS-ASSOCIATED FATTY ACID-BINDING PROTEIN HOMOLOG) (PA-FABP). [SWISSPROT;Acc:Q01469]"	0.0334849	0.110947	0.301809873
294	"BETA-CAROTENE DIOXYGENASE 2; PUTATIVE B,B-CAROTENE-9',10'-DIOXYGENASE. [RefSeq;Acc:NM_031938]"	0.0429558	0.142328	0.301808499
303	HPAII TINY FRAGMENTS LOCUS 9C. [RefSeq;Acc:NM_022727]	0.20849	0.697153	0.299059174
304	UBIQUITIN. [SWISSPROT;Acc:P02248]	0.241123	0.807018	0.298782679
306	ALPHA-1-ACID GLYCOPROTEIN 2 PRECURSOR (AGP 2) (OROSOMUCOID 2) (OMD 2). [SWISSPROT;Acc:P19652]	0.232016	0.784548	0.295732065
308	MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S32 (S32MT) (MRP-S32) (PTD007) (HSPC204). [SWISSPROT;Acc:Q9Y6G3]	0.0503334	0.170278	0.295595438
313	BA395L14.12 (NOVEL PROTEIN SIMILAR TO SMALL NUCLEAR RIBONUCLEOPROTEIN POLYPEPTIDE A' (SNRPA1)). [SPTREMBL;Acc:Q9NU36]	0.482398	1.63545	0.294963466
333	GA BINDING PROTEIN BETA-2 CHAIN (GABP-BETA-2 SUBUNIT) (TRANSCRIPTION FACTOR E4TF1-47) (GAPBP-2) (NUCLEAR RESPIRATORY FACTOR-2 SUBUNIT GAMMA). [SWISSPROT;Acc:Q06545]	0.0373117	0.130845	0.28515954
347		0.135144	0.478436	0.282470383
356		0.0483186	0.171674	0.281455549
357		0.042516	0.151058	0.281454805
373		0.034272	0.122748	0.279206179
392	40S RIBOSOMAL PROTEIN S26. [SWISSPROT;Acc:P02383]	0.135061	0.484774	0.278606113
411		0.356784	1.28488	0.277678849
425	DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 47; HQP0256 PROTEIN. [RefSeq;Acc:NM_016355]	0.0884193	0.318777	0.277370387
438	TRANSFORMER-2 PROTEIN HOMOLOG (TRA-2 ALPHA). [SWISSPROT;Acc:Q13595]	0.345566	1.24774	0.276953532
452	"PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 (EC 3.1.3.48) (PROTEIN-TYROSINE PHOSPHATASE 1B) (PTP-1B). [SWISSPROT;Acc:P18031]"	0.215243	0.779889	0.27599184
460	COLLAGEN ALPHA 5(IV) CHAIN PRECURSOR. [SWISSPROT;Acc:P29400]	0.0637349	0.231274	0.27558177699999997
492		0.0344618	0.125634	0.274303135
498		0.236585	0.862726	0.274229593

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
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots