[Genome] expIds

Thu Apr 3 09:45:04 PDT 2008

Hello Sonja,

	Sorry that I misunderstood your question.  Yes, you have understood the 
relationship between the table and the display correctly.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

sonja althammer wrote:
> hello!
> thanks, but i already got the table you printed for me...
> my question refered to something else:
> in the table hgFixed.gnfHumanAtlas2AllExps there are IDs in the range from 0 to 157 while there are just 79 expIds for human in the gnf atlas2 for expression and  regulation.
> for mouse it is analog...
> so is it correct to conclude that
> 
> 0 ColorectalAdenocarcinoma         and 
> 1 ColorectalAdenocarcinoma 2
> refer to the exprId 1
> 
> 2,3 refer to  exprId 2
> 4,5 refer to exprId 3
> ...
> 156,157 refer to  exprId 78
> 
> you understand what i mean?
> basically i need to get the expression-values from all common tissues in mouse and human or rather the conservation of the expression in all common tissues...
> best regards!
> sonja
> 
> 
> 
> Ann Zweig <ann at soe.ucsc.edu> wrote: Hello again Sonja,
> 
>  I have printed the contents of the tables for your use (see below).  This 
> should help you correlate between mouse and human.
> 
>  In the future, please direct your questions to the genome mailing list at 
> genome at soe.ucsc.edu -- our moderated forum for user questions and discussion. 
> You will likely get a quicker response to your question.
> 
> 
> Regards,
> 
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
> 
> 
> hgFixed.gnfMouseAtlas2AllExps
> #id name
> 0 substantia nigra
> 1 substantia nigra 2
> 2 spinal cord upper
> 3 spinal cord upper 2
> 4 spinal cord lower
> 5 spinal cord lower 2
> 6 hypothalamus
> 7 hypothalamus 2
> 8 preoptic
> 9 preoptic 2
> 10 frontal cortex
> 11 frontal cortex 2
> 12 cerebral cortex
> 13 cerebral cortex 2
> 14 amygdala
> 15 amygdala 2
> 16 dorsal striatum
> 17 dorsal striatum 2
> 18 hippocampus
> 19 hippocampus 2
> 20 olfactory bulb
> 21 olfactory bulb 2
> 22 cerebellum
> 23 cerebellum 2
> 24 trigeminal
> 25 trigeminal 2
> 26 dorsal root ganglia
> 27 dorsal root ganglia 2
> 28 pituitary
> 29 pituitary 2
> 30 eye
> 31 eye 2
> 32 lymph node
> 33 lymph node 2
> 34 trachea
> 35 trachea 2
> 36 uterus
> 37 uterus 2
> 38 ovary
> 39 ovary 2
> 40 adipose tissue
> 41 adipose tissue 2
> 42 adrenal gland
> 43 adrenal gland 2
> 44 bladder
> 45 bladder 2
> 46 embryo day 10.5
> 47 embryo day 10.5 2
> 48 embryo day 9.5
> 49 embryo day 9.5 2
> 50 embryo day 8.5
> 51 embryo day 8.5 2
> 52 embryo day 7.5
> 53 embryo day 7.5 2
> 54 embryo day 6.5
> 55 embryo day 6.5 2
> 56 epidermis
> 57 epidermis 2
> 58 digits
> 59 digits 2
> 60 snout epidermis
> 61 snout epidermis 2
> 62 tongue
> 63 tongue 2
> 64 medial olfactory epithelium
> 65 medial olfactory epithelium 2
> 66 prostate
> 67 prostate 2
> 68 vomeralnasal organ
> 69 vomeralnasal organ 2
> 70 lung
> 71 lung 2
> 72 umbilical cord
> 73 umbilical cord 2
> 74 stomach
> 75 stomach 2
> 76 large intestine
> 77 large intestine 2
> 78 bone marrow
> 79 bone marrow 2
> 80 bone
> 81 bone 2
> 82 spleen
> 83 spleen 2
> 84 thymus
> 85 thymus 2
> 86 B220+ B-cells
> 87 B220+ B-cells 2
> 88 CD4+T-cells
> 89 CD4+T-cells 2
> 90 CD8+T-cells
> 91 CD8+T-cells 2
> 92 brown fat
> 93 brown fat 2
> 94 heart
> 95 heart 2
> 96 skeletal muscle
> 97 skeletal muscle 2
> 98 placenta
> 99 placenta 2
> 100 mammary gland (lact)
> 101 mammary gland (lact) 2
> 102 blastocysts
> 103 blastocysts 2
> 104 kidney
> 105 kidney 2
> 106 small intestine
> 107 small intestine 2
> 108 salivary gland
> 109 salivary gland 2
> 110 thyroid
> 111 thyroid 2
> 112 liver
> 113 liver 2
> 114 fertilized egg
> 115 fertilized egg 2
> 116 oocyte
> 117 oocyte 2
> 118 pancreas
> 119 pancreas 2
> 120 testis
> 121 testis 2
> 
> 
> hgFixed.gnfHumanAtlas2AllExps
> #id name
> 0 ColorectalAdenocarcinoma
> 1 ColorectalAdenocarcinoma 2
> 2 WHOLEBLOOD
> 3 WHOLEBLOOD 2
> 4 BM-CD33+Myeloid
> 5 BM-CD33+Myeloid 2
> 6 PB-CD14+Monocytes
> 7 PB-CD14+Monocytes 2
> 8 PB-BDCA4+Dentritic Cells
> 9 PB-BDCA4+Dentritic Cells 2
> 10 PB-CD56+NKCells
> 11 PB-CD56+NKCells 2
> 12 PB-CD4+Tcells
> 13 PB-CD4+Tcells 2
> 14 PB-CD8+Tcells
> 15 PB-CD8+Tcells 2
> 16 PB-CD19+Bcells
> 17 PB-CD19+Bcells 2
> 18 BM-CD105+Endothelial
> 19 BM-CD105+Endothelial 2
> 20 BM-CD34+
> 21 BM-CD34+ 2
> 22 leukemialymphoblastic(molt4)
> 23 leukemialymphoblastic(molt4) 2
> 24 721 B lymphoblasts
> 25 721 B lymphoblasts 2
> 26 lymphomaburkittsRaji
> 27 lymphomaburkittsRaji 2
> 28 leukemiapromyelocytic(hl60)
> 29 leukemiapromyelocytic(hl60) 2
> 30 lymphomaburkittsDaudi
> 31 lymphomaburkittsDaudi 2
> 32 leukemiachronicmyelogenous(k562)
> 33 leukemiachronicmyelogenous(k562) 2
> 34 thymus
> 35 thymus 2
> 36 Tonsil
> 37 Tonsil 2
> 38 lymphnode
> 39 lymphnode 2
> 40 fetalliver
> 41 fetalliver 2
> 42 BM-CD71+EarlyErythroid
> 43 BM-CD71+EarlyErythroid 2
> 44 bonemarrow
> 45 bonemarrow 2
> 46 TemporalLobe
> 47 TemporalLobe 2
> 48 globuspallidus
> 49 globuspallidus 2
> 50 CerebellumPeduncles
> 51 CerebellumPeduncles 2
> 52 cerebellum
> 53 cerebellum 2
> 54 caudatenucleus
> 55 caudatenucleus 2
> 56 WholeBrain
> 57 WholeBrain 2
> 58 ParietalLobe
> 59 ParietalLobe 2
> 60 MedullaOblongata
> 61 MedullaOblongata 2
> 62 Amygdala
> 63 Amygdala 2
> 64 PrefrontalCortex
> 65 PrefrontalCortex 2
> 66 OccipitalLobe
> 67 OccipitalLobe 2
> 68 Hypothalamus
> 69 Hypothalamus 2
> 70 Thalamus
> 71 Thalamus 2
> 72 subthalamicnucleus
> 73 subthalamicnucleus 2
> 74 CingulateCortex
> 75 CingulateCortex 2
> 76 Pons
> 77 Pons 2
> 78 spinalcord
> 79 spinalcord 2
> 80 fetalbrain
> 81 fetalbrain 2
> 82 adrenalgland
> 83 adrenalgland 2
> 84 Lung
> 85 Lung 2
> 86 Heart
> 87 Heart 2
> 88 Liver
> 89 Liver 2
> 90 kidney
> 91 kidney 2
> 92 Prostate
> 93 Prostate 2
> 94 Uterus
> 95 Uterus 2
> 96 Thyroid
> 97 Thyroid 2
> 98 fetalThyroid
> 99 fetalThyroid 2
> 100 fetallung
> 101 fetallung 2
> 102 PLACENTA
> 103 PLACENTA 2
> 104 CardiacMyocytes
> 105 CardiacMyocytes 2
> 106 SmoothMuscle
> 107 SmoothMuscle 2
> 108 bronchialepithelialcells
> 109 bronchialepithelialcells 2
> 110 ADIPOCYTE
> 111 ADIPOCYTE 2
> 112 Pancreas
> 113 Pancreas 2
> 114 PancreaticIslets
> 115 PancreaticIslets 2
> 116 testis
> 117 testis 2
> 118 TestisLeydigCell
> 119 TestisLeydigCell 2
> 120 TestisGermCell
> 121 TestisGermCell 2
> 122 TestisInterstitial
> 123 TestisInterstitial 2
> 124 TestisSeminiferousTubule
> 125 TestisSeminiferousTubule 2
> 126 salivarygland
> 127 salivarygland 2
> 128 trachea
> 129 trachea 2
> 130 AdrenalCortex
> 131 AdrenalCortex 2
> 132 Ovary
> 133 Ovary 2
> 134 Appendix
> 135 Appendix 2
> 136 skin
> 137 skin 2
> 138 ciliaryganglion
> 139 ciliaryganglion 2
> 140 TrigeminalGanglion
> 141 TrigeminalGanglion 2
> 142 atrioventricularnode
> 143 atrioventricularnode 2
> 144 DRG
> 145 DRG 2
> 146 SuperiorCervicalGanglion
> 147 SuperiorCervicalGanglion 2
> 148 SkeletalMuscle
> 149 SkeletalMuscle 2
> 150 UterusCorpus
> 151 UterusCorpus 2
> 152 TONGUE
> 153 TONGUE 2
> 154 OlfactoryBulb
> 155 OlfactoryBulb 2
> 156 Pituitary
> 157 Pituitary 2
> 
> sonja althammer wrote:
>> hello ann!
>> thanks a lot! i found the tables i was looking for!
>> but what i still do not understand about the tables is, why #id (in 
>> hgFixed.gnfHumanAtlas2AllExps) is in the range from 0 to 157 while there 
>> are just 79 expIds for human in the gnf atlas2 for expression and 
>> regulation.
>> for mouse it is analog...
>> as the tissues appear twice, do i conclude right like this:
>> to get the according tissue to expId 79 i select #id 156 from 
>> hgFixed.gnfHumanAtlas2AllExps (expId*2 -2)
>>
>> in the end i want to work with the intersection of the tissues in human 
>> and mouse...
>> best regards!
>> sonja
>>
>> */Ann Zweig /* wrote:
>>
>>     Hello Sonja,
>>
>>     You can find the tissue types for each of the GNF Atlas 2 tracks in the
>>     corresponding tables in the hgFixed database:
>>
>>     gnfHumanAtlas2AllExps
>>     gnfMouseAtlas2AllExps
>>
>>     To explore the contents of database tables, use the Table Browser tool
>>     on the website ('Tables' from the top blue navigation bar).
>>
>>     group: All Tables
>>     database: hgFixed
>>     table: hgFixed.gnfHumanAtlas2AllExps
>>
>>     output format: all fields from selected table
>>
>>     The id and name fields contain the information you are looking for.
>>     For example, from the hgFixed.gnfHumanAtlas2AllExps table, the first 5
>>     rows are:
>>
>>     #id name
>>     0 ColorectalAdenocarcinoma
>>     1 ColorectalAdenocarcinoma 2
>>     2 WHOLEBLOOD
>>     3 WHOLEBLOOD 2
>>     4 BM-CD33+Myeloid
>>
>>
>>     You might also be interested in reading the paper associated with this
>>     track: http://www.pnas.org/cgi/content/abstract/101/16/6062
>>
>>     I hope this information is helpful to you. Please don't hesitate to
>>     contact the mail list again if you require further assistance.
>>
>>     Regards,
>>
>>     ----------
>>     Ann Zweig
>>     UCSC Genome Bioinformatics Group
>>     http://genome.ucsc.edu
>>
>>     Please feel free to search the Genome mailing list archives by visiting
>>     our home page, clicking on "Contact Us", then typing a word or phrase
>>     into the search box. On that same page
>>     (http://genome.ucsc.edu/contacts.html), you can subscribe to the Genome
>>     mailing list.
>>
>>
>>
>>
>>
>>
>>     sonja althammer wrote:
>>      > browsing the expression data from the gnf atlas2 my question arose:
>>      > are the expression-Ids equal for human and mouse, i.e. do they
>>     refer to the same type of tissue?
>>      > best regards!
>>      >
>>      >
>>      > ---------------------------------
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>>      > _______________________________________________
>>      > Genome maillist - Genome at soe.ucsc.edu
>>      > http://www.soe.ucsc.edu/mailman/listinfo/genome
>>
>>
>> ------------------------------------------------------------------------
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> 
>        
> ---------------------------------
> You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost.
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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