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.

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Rank	measured	Gene	description	Hugo	expected	final

Results: HTML CSV LaTeX

Showing element 501 to 550 of 3206 in total

Rank	measured	description	Hugo	expected	final
501	0.281309	SPECTRIN SH3 DOMAIN BINDING PROTEIN 1; EPS8 BINDING PROTEIN; INTERACTOR PROTEIN ABLBP4; ABL-INTERACTOR PROTEIN 1 LONG; NAP1 BINDING PROTEIN. [RefSeq;Acc:NM_005470]	ABI1	1.0262	0.274126876
502	0.0401445		CDV3	0.146476	0.274068789
503	0.367035	EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 7 (EIF-3 ZETA) (EIF3 P66) (EIF3D). [SWISSPROT;Acc:O15371]	EIF3D	1.33921	0.274068294
504	0.0286746	ENIGMA PROTEIN; LIM DOMAIN PROTEIN. [RefSeq;Acc:NM_005451]	no value	0.104626	0.274067631
505	0.183159	INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 1 (EC 1.1.1.205) (IMP DEHYDROGENASE 1) (IMPDH-I) (IMPD 1). [SWISSPROT;Acc:P20839]	IMPDH1	0.66836	0.274042432
506	0.157432	INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 2 (EC 1.1.1.205) (IMP DEHYDROGENASE 2) (IMPDH-II) (IMPD 2). [SWISSPROT;Acc:P12268]	IMPDH2	0.574482	0.274041658
507	0.348668	GMP SYNTHASE [GLUTAMINE-HYDROLYZING] (EC 6.3.5.2) (GLUTAMINE AMIDOTRANSFERASE) (GMP SYNTHETASE). [SWISSPROT;Acc:P49915]	GMPS	1.27232	0.274041122
508	0.135095	HEAT SHOCK FACTOR BINDING PROTEIN 1. [SWISSPROT;Acc:O75506]	no value	0.493083	0.273980243
509	0.0968147	"RNA, U TRANSPORTER 1; SNURPORTIN-1. [RefSeq;Acc:NM_005701]"	SNUPN	0.353554	0.273832852
510	0.250323		KIAA1217	0.914445	0.27374309
511	0.131932	PROTEIN KINASE CLK2 (EC 2.7.1.-) (CDC-LIKE KINASE 2). [SWISSPROT;Acc:P49760]	CLK2	0.482648	0.273350351
512	0.1005	PROTEIN KINASE CLK3 (EC 2.7.1.-) (CDC-LIKE KINASE 3). [SWISSPROT;Acc:P49761]	CLK3	0.367745	0.273287196
513	0.541777	NUCLEAR PROTEIN SKIP (SKI-INTERACTING PROTEIN) (SNW1 PROTEIN) (NUCLEAR RECEPTOR COACTIVATOR NCOA-62). [SWISSPROT;Acc:Q13573]	SNW1	1.98406	0.273064827
514	0.424547	RNA-BINDING PROTEIN 9 (RNA BINDING MOTIF PROTEIN 9) (HEXARIBONUCLEOTIDE BINDING PROTEIN 2) (REPRESSOR OF TAMOXIFEN TRANSCRIPTIONAL ACTIVITY). [SWISSPROT;Acc:O43251]	RBM9	1.55794	0.27250536
515	0.534301	ATAXIN 2-BINDING PROTEIN. [SWISSPROT;Acc:Q9NWB1]	no value	1.96129	0.272423252
516	0.0480412		METT10D	0.176368	0.272391817
517	0.313715		UBAP2L	1.15171	0.272390619
518	0.510382	M-PHASE INDUCER PHOSPHATASE 2 (EC 3.1.3.48) (DUAL SPECIFICITY PHOSPHATASE CDC25B). [SWISSPROT;Acc:P30305]	CDC25B	1.8743	0.272305394
519	0.0379775	"BREAST CARCINOMA AMPLIFIED SEQUENCE 2; SPLICEOSOME ASSOCIATED PROTEIN, AMPLIFIED IN BREAST CANCER. [RefSeq;Acc:NM_005872]"	BCAS2	0.139495	0.272249901
520	0.333016	"CDC5-LIKE; CDC5 (CELL DIVISION CYCLE 5, S. POMBE, HOMOLOG)-LIKE; CELL DIVISION CYCLE 5, S. POMBE, HOMOLOG-LIKE; CDC5-RELATED PROTEIN. [RefSeq;Acc:NM_001253]"	CDC5L	1.2232	0.272249836
521	0.504359	RNA-BINDING PROTEIN WITH MULTIPLE SPLICING (RBP-MS). [SWISSPROT;Acc:Q93062]	RBPMS	1.85404	0.272032426
522	0.694134	"PRE-MRNA CLEAVAGE FACTOR I, 59 KDA SUBUNIT. [RefSeq;Acc:NM_024811]"	no value	2.5522	0.271974767
523	0.142881	"1,4-ALPHA-GLUCAN BRANCHING ENZYME (EC 2.4.1.18) (GLYCOGEN BRANCHING ENZYME) (BRANCHER ENZYME). [SWISSPROT;Acc:Q04446]"	GBE1	0.525483	0.271904134
524	0.0229997	"GLYCOGEN PHOSPHORYLASE, MUSCLE FORM (EC 2.4.1.1) (MYOPHOSPHORYLASE). [SWISSPROT;Acc:P11217]"	PYGM	0.0845876	0.27190392
525	0.0231429	"GLYCOGEN PHOSPHORYLASE, BRAIN FORM (EC 2.4.1.1). [SWISSPROT;Acc:P11216]"	PYGB	0.0851144	0.271903462
526	0.0249116	MYOSIN XV (UNCONVENTIONAL MYOSIN-15). [SWISSPROT;Acc:Q9UKN7]	MYO15A	0.0916194	0.271903112
527		"GLYCOGEN PHOSPHORYLASE, LIVER FORM (EC 2.4.1.1). [SWISSPROT;Acc:P06737]"	PYGL
528	0.309836	"PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 12B ISOFORM A; MYOSIN PHOSPHATASE REGULATORY SUBUNIT; MYOSIN PHOSPHATASE, TARGET SUBUNIT 2. [RefSeq;Acc:NM_002481]"	PPP1R12B	1.13987	0.271816962
529	0.253813	"PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 12A; MYOSIN PHOSPHATASE, TARGET SUBUNIT 1. [RefSeq;Acc:NM_002480]"	PPP1R12A	0.933978	0.271754795
530	0.260139		RBM24	0.957852	0.271585798
531	0.216511	RNA-BINDING REGION CONTAINING PROTEIN 1 (HSRNASEB) (SSDNA BINDING PROTEIN SEB4) (CLL-ASSOCIATED ANTIGEN KW-5). [SWISSPROT;Acc:Q9H0Z9]	RBM38	0.797256	0.271570236
532	0.404881	"KARYOPHERIN BETA 2B, TRANSPORTIN; IMPORTIN 3. [RefSeq;Acc:NM_013433]"	TNPO2	1.49189	0.271387971
533	0.232461	SMALL NUCLEAR RIBONUCLEOPROTEIN F (SNRNP-F) (SM PROTEIN F) (SM-F) (SMF). [SWISSPROT;Acc:Q15356]	SNRPF	0.856628	0.271367501
534	0.0399967	SMALL NUCLEAR RIBONUCLEOPROTEIN E (SNRNP-E) (SM PROTEIN E) (SM-E) (SME). [SWISSPROT;Acc:P08578]	no value	0.14739	0.271366443
535	0.443276	IMPORTIN BETA-2 SUBUNIT (KARYOPHERIN BETA-2 SUBUNIT) (TRANSPORTIN) (M9 REGION INTERACTION PROTEIN) (MIP). [SWISSPROT;Acc:Q92973]	TNPO1	1.63446	0.271206392
536	0.122154	BROMODOMAIN-CONTAINING PROTEIN 3 (RING3-LIKE PROTEIN). [SWISSPROT;Acc:Q15059]	BRD3	0.450566	0.271112334
537	0.105783	BROMODOMAIN-CONTAINING PROTEIN 2 (RING3 PROTEIN) (O27.1.1). [SWISSPROT;Acc:P25440]	BRD2	0.390223	0.271083457
538	0.144761	BROMODOMAIN-CONTAINING PROTEIN 4 (HUNK1 PROTEIN). [SWISSPROT;Acc:O60885]	BRD4	0.534019	0.27107837
539	0.0778103		SRBD1	0.28704	0.271078247
540	0.0358609		LRRC4B	0.13229	0.271077935
541	0.0376313	NAG14 PROTEIN. [RefSeq;Acc:NM_022143]	LRRC4	0.138821	0.271077863
542	0.152328	PROTEIN REGULATOR OF CYTOKINESIS 1; PROTEIN REGULATING CYTOKINESIS 1. [RefSeq;Acc:NM_003981]	no value	0.561935	0.271077616
543	0.0431799		LRRC4C	0.15929	0.27107728
544	0.0996239	TESTIS-SPECIFIC BROMODOMAIN PROTEIN. [RefSeq;Acc:NM_001726]	BRDT	0.36752	0.27107069
545	0.59995	QUAKING ISOFORM 6. [SPTREMBL;Acc:Q9P0X9]	QKI	2.2133	0.271065829
546	0.0497647	ABHYDROLASE DOMAIN CONTAINING PROTEIN 2 (PROTEIN PHPS1-2). [SWISSPROT;Acc:P08910]	ABHD2	0.183589	0.271065805
547	0.24526	"CUG TRIPLET REPEAT, RNA BINDING PROTEIN 2; ELAV-TYPE RNA-BINDING PROTEIN; CUG TRIPLET REPEAT,RNA-BINDING PROTEIN 2; CUG TRIPLET REPEAT, RNA-BINDING PROTEIN 2; NEUROBLASTOMA APOPTOSIS-RELATED RNA-BINDING PROTEIN. [RefSeq;Acc:NM_006561]"	CUGBP2	0.905006	0.271003728
548	0.267337	CUG TRIPLET REPEAT RNA-BINDING PROTEIN 1 (CUG-BP1) (RNA-BINDING PROTEIN BRUNOL-2) (DEADENYLATION FACTOR CUG-BP) (50 KDA NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN) (EDEN-BP). [SWISSPROT;Acc:Q92879]	CUGBP1	0.986471	0.271003405
549	0.046789	SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH PROTEIN (SH3BGR PROTEIN) (21- GLUTAMIC ACID-RICH PROTEIN) (21-GARP). [SWISSPROT;Acc:P55822]	SH3BGR	0.172653	0.271000214
550		LATS HOMOLOG 1. [RefSeq;Acc:NM_004690]	LATS1

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